Reset repository and upload final project (part 5)

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_130501.dtd

@@ -0,0 +1,79 @@
+<!--    
+	   This is the Current DTD which NLM has written for 
+        External  Use.  If you are a NCBI User, use the information
+        from the PubmedArticleSet.
+
+        Comments and suggestions are welcome.
+        (May 9, 2000)
+	
+        Corrections:
+        ~~~~~~~~~~~
+        Oct. 09 2002 
+        - "PubMedArticle" has been renamed to "PubmedArticle"
+        - All referencies to "PubMedArticle" has been removed
+        - "ProviderId" has been removed from PubmedData
+        - "URL" has been removed from PubmdeData
+		
+		$Id: pubmed_130501.dtd 404126 2013-06-20 17:36:43Z korobtch $
+        
+       -->
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!-- Reference to Where the MEDLINECITATION DTD is located  -->
+<!ENTITY % Medline PUBLIC "-//NLM//DTD Medline, 01 May 2013//EN"
+      "nlmmedlinecitationset_130501.dtd">
+%Medline;
+<!-- ================================================================= -->
+<!ENTITY % ArticleTitle.Ref "ArticleTitle">
+<!ENTITY % ISSN.Ref "ISSN?">
+<!ENTITY % Pub.Date.Ref "PubDate?">
+<!ENTITY % iso.language.codes "(AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                                   HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                                   PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                                   VI|ZH)">
+<!ENTITY % pub.status.int "pmc | pmcr | pubmed | pubmedr | 
+                             premedline | medline | medliner | entrez | pmc-release">
+<!ENTITY % pub.status "(received | accepted | epublish | 
+                              ppublish | revised | aheadofprint | 
+                              retracted | ecollection | %pub.status.int;)">
+<!ENTITY % art.id.type.int "pubmed | medline | pmcid | pmcbook | bookaccession">
+							
+<!ENTITY % art.id.type "(doi | pii | pmcpid | pmpid | pmc | mid |
+                              sici | %art.id.type.int;)">
+<!-- ================================================================= -->
+<!ELEMENT PubmedArticleSet (PubmedArticle | PubmedBookArticle)+>
+<!-- ================================================================= -->
+<!-- This is the top level element for PubMedArticle -->
+<!ELEMENT PubmedArticle (MedlineCitation, PubmedData?)>
+<!-- ================================================================= -->
+<!ENTITY % normal.date "Year, Month, Day, (Hour, (Minute, Second?)?)?">
+<!ELEMENT PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+<!ELEMENT PubMedPubDate (%normal.date;)>
+<!ATTLIST PubMedPubDate
+	PubStatus %pub.status; #REQUIRED
+>
+<!ELEMENT PublicationStatus (#PCDATA)>
+<!ELEMENT ArticleIdList (ArticleId+)>
+<!ELEMENT ArticleId (#PCDATA)>
+<!ATTLIST ArticleId
+	IdType %art.id.type; "pubmed"
+>
+<!ELEMENT History (PubMedPubDate+)>
+<!ELEMENT URL (#PCDATA)>
+<!ATTLIST URL
+	lang %iso.language.codes; #IMPLIED
+	Type ( FullText | Summary | fulltext | summary) #IMPLIED
+>
+<!ELEMENT ObjectList (Object)+>
+<!ELEMENT Object (Param)*>
+<!ATTLIST Object Type CDATA #REQUIRED>
+<!ELEMENT Param %text;>
+<!ATTLIST Param Name CDATA #REQUIRED>
+<!ELEMENT Hour (#PCDATA)>
+<!ELEMENT Minute (#PCDATA)>
+<!ELEMENT Second (#PCDATA)>
+
+<!-- ================================================================= -->
+<!ENTITY % Bookdoc PUBLIC "-//NLM//DTD Bookdoc, 01 Jan 2013//EN" "bookdoc_130101.dtd">
+%Bookdoc;
+<!-- ================================================================= -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_140101.dtd

@@ -0,0 +1,79 @@
+<!--    
+	   This is the Current DTD which NLM has written for 
+        External  Use.  If you are a NCBI User, use the information
+        from the PubmedArticleSet.
+
+        Comments and suggestions are welcome.
+        (May 9, 2000)
+	
+        Corrections:
+        ~~~~~~~~~~~
+        Oct. 09 2002 
+        - "PubMedArticle" has been renamed to "PubmedArticle"
+        - All referencies to "PubMedArticle" has been removed
+        - "ProviderId" has been removed from PubmedData
+        - "URL" has been removed from PubmdeData
+		
+		$Id: pubmed_140101.dtd 413871 2013-09-18 19:22:41Z korobtch $
+        
+       -->
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!-- Reference to Where the MEDLINECITATION DTD is located  -->
+<!ENTITY % Medline PUBLIC "-//NLM//DTD Medline, 01 Jan 2014//EN"
+      "nlmmedlinecitationset_140101.dtd">
+%Medline;
+<!-- ================================================================= -->
+<!ENTITY % ArticleTitle.Ref "ArticleTitle">
+<!ENTITY % ISSN.Ref "ISSN?">
+<!ENTITY % Pub.Date.Ref "PubDate?">
+<!ENTITY % iso.language.codes "(AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                                   HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                                   PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                                   VI|ZH)">
+<!ENTITY % pub.status.int "pmc | pmcr | pubmed | pubmedr | 
+                             premedline | medline | medliner | entrez | pmc-release">
+<!ENTITY % pub.status "(received | accepted | epublish | 
+                              ppublish | revised | aheadofprint | 
+                              retracted | ecollection | %pub.status.int;)">
+<!ENTITY % art.id.type.int "pubmed | medline | pmcid | pmcbook | bookaccession">
+							
+<!ENTITY % art.id.type "(doi | pii | pmcpid | pmpid | pmc | mid |
+                              sici | %art.id.type.int;)">
+<!-- ================================================================= -->
+<!ELEMENT PubmedArticleSet (PubmedArticle | PubmedBookArticle)+>
+<!-- ================================================================= -->
+<!-- This is the top level element for PubMedArticle -->
+<!ELEMENT PubmedArticle (MedlineCitation, PubmedData?)>
+<!-- ================================================================= -->
+<!ENTITY % normal.date "Year, Month, Day, (Hour, (Minute, Second?)?)?">
+<!ELEMENT PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+<!ELEMENT PubMedPubDate (%normal.date;)>
+<!ATTLIST PubMedPubDate
+	PubStatus %pub.status; #REQUIRED
+>
+<!ELEMENT PublicationStatus (#PCDATA)>
+<!ELEMENT ArticleIdList (ArticleId+)>
+<!ELEMENT ArticleId (#PCDATA)>
+<!ATTLIST ArticleId
+	IdType %art.id.type; "pubmed"
+>
+<!ELEMENT History (PubMedPubDate+)>
+<!ELEMENT URL (#PCDATA)>
+<!ATTLIST URL
+	lang %iso.language.codes; #IMPLIED
+	Type ( FullText | Summary | fulltext | summary) #IMPLIED
+>
+<!ELEMENT ObjectList (Object)+>
+<!ELEMENT Object (Param)*>
+<!ATTLIST Object Type CDATA #REQUIRED>
+<!ELEMENT Param %text;>
+<!ATTLIST Param Name CDATA #REQUIRED>
+<!ELEMENT Hour (#PCDATA)>
+<!ELEMENT Minute (#PCDATA)>
+<!ELEMENT Second (#PCDATA)>
+
+<!-- ================================================================= -->
+<!ENTITY % Bookdoc PUBLIC "-//NLM//DTD Bookdoc, 01 Jan 2014//EN" "bookdoc_140101.dtd">
+%Bookdoc;
+<!-- ================================================================= -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_150101.dtd

@@ -0,0 +1,79 @@
+<!--    
+	   This is the Current DTD which NLM has written for 
+        External  Use.  If you are a NCBI User, use the information
+        from the PubmedArticleSet.
+
+        Comments and suggestions are welcome.
+        (May 9, 2000)
+	
+        Corrections:
+        ~~~~~~~~~~~
+        Oct. 09 2002 
+        - "PubMedArticle" has been renamed to "PubmedArticle"
+        - All referencies to "PubMedArticle" has been removed
+        - "ProviderId" has been removed from PubmedData
+        - "URL" has been removed from PubmdeData
+		
+		$Id: pubmed_150101.dtd 447938 2014-10-01 17:41:38Z korobtch $
+        
+       -->
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!-- Reference to Where the MEDLINECITATION DTD is located  -->
+<!ENTITY % Medline PUBLIC "-//NLM//DTD Medline, 01 Jan 2015//EN"
+      "nlmmedlinecitationset_150101.dtd">
+%Medline;
+<!-- ================================================================= -->
+<!ENTITY % ArticleTitle.Ref "ArticleTitle">
+<!ENTITY % ISSN.Ref "ISSN?">
+<!ENTITY % Pub.Date.Ref "PubDate?">
+<!ENTITY % iso.language.codes "(AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                                   HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                                   PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                                   VI|ZH)">
+<!ENTITY % pub.status.int "pmc | pmcr | pubmed | pubmedr | 
+                             premedline | medline | medliner | entrez | pmc-release">
+<!ENTITY % pub.status "(received | accepted | epublish | 
+                              ppublish | revised | aheadofprint | 
+                              retracted | ecollection | %pub.status.int;)">
+<!ENTITY % art.id.type.int "pubmed | medline | pmcid | pmcbook | bookaccession">
+							
+<!ENTITY % art.id.type "(doi | pii | pmcpid | pmpid | pmc | mid |
+                              sici | %art.id.type.int;)">
+<!-- ================================================================= -->
+<!ELEMENT PubmedArticleSet (PubmedArticle | PubmedBookArticle)+>
+<!-- ================================================================= -->
+<!-- This is the top level element for PubMedArticle -->
+<!ELEMENT PubmedArticle (MedlineCitation, PubmedData?)>
+<!-- ================================================================= -->
+<!ENTITY % normal.date "Year, Month, Day, (Hour, (Minute, Second?)?)?">
+<!ELEMENT PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+<!ELEMENT PubMedPubDate (%normal.date;)>
+<!ATTLIST PubMedPubDate
+	PubStatus %pub.status; #REQUIRED
+>
+<!ELEMENT PublicationStatus (#PCDATA)>
+<!ELEMENT ArticleIdList (ArticleId+)>
+<!ELEMENT ArticleId (#PCDATA)>
+<!ATTLIST ArticleId
+	IdType %art.id.type; "pubmed"
+>
+<!ELEMENT History (PubMedPubDate+)>
+<!ELEMENT URL (#PCDATA)>
+<!ATTLIST URL
+	lang %iso.language.codes; #IMPLIED
+	Type ( FullText | Summary | fulltext | summary) #IMPLIED
+>
+<!ELEMENT ObjectList (Object)+>
+<!ELEMENT Object (Param)*>
+<!ATTLIST Object Type CDATA #REQUIRED>
+<!ELEMENT Param %text;>
+<!ATTLIST Param Name CDATA #REQUIRED>
+<!ELEMENT Hour (#PCDATA)>
+<!ELEMENT Minute (#PCDATA)>
+<!ELEMENT Second (#PCDATA)>
+
+<!-- ================================================================= -->
+<!ENTITY % Bookdoc PUBLIC "-//NLM//DTD Bookdoc, 01 Jan 2015//EN" "bookdoc_150101.dtd">
+%Bookdoc;
+<!-- ================================================================= -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_180101.dtd

@@ -0,0 +1,434 @@
+<!--
+
+2017-10-06
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd
+
+Additions/Changes since 170101 DTD: 
+
+	1.  Added Organism to the allowed values for SupplMeshName @Type
+	2.  Deleted DateCreated
+
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE:  StartPage and EndPage in Pagination element are not currently used; are 
+	reserved for future use. 
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "(#PCDATA | b | i | sup | sub | u)*" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, CitationString?, GrantList?, ItemList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText %text;>
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation %text;>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle %text;>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		%text; > <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle      %text; >
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	CitationString      %text; >
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement    %text; >
+
+<!ELEMENT	CollectionTitle      %text; >
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName %text; >
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | AssociatedPublication | CommentOn | CommentIn | ErratumIn | 
+		             ErratumFor | ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedFrom | RepublishedIn | 
+		             RetractionOf | RetractionIn | UpdateIn | UpdateOf | SummaryForPatientsIn | 
+		             OriginalReportIn | ReprintOf | ReprintIn | Cites)      #REQUIRED    >
+		             
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		%text; > <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword %text;>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param %text;>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName      %text; >
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	%text; >
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	%text; > <!-- subscript -->
+
+<!ELEMENT	Suffix %text;>
+
+<!ELEMENT	sup	%text; > <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type (Disease | Protocol | Organism) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		%text; > <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle %text; >
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle %text; >
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_180601.dtd

@@ -0,0 +1,454 @@
+<!--
+
+2017-10-06
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180101.dtd
+
+Additions/Changes since 180101 DTD: 
+
+	1.  Added MathML3 
+	2.  Allowed <mml:math> in <AbstractText>, <ArticleTitle>, <BookTitle>, <CollectionTitle>, 
+	     <Keyword>, <VernacularTitle>.
+
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE:  StartPage and EndPage in Pagination element are not currently used; are 
+	reserved for future use. 
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+       
+<!-- ============================================================= -->
+<!--                     MATHML 3.0 SETUP                        -->
+<!-- ============================================================= -->
+<!--                    MATHML SETUP FILE                 -->
+<!ENTITY % mathml-in-pubmed     SYSTEM        "mathml-in-pubmed.mod"               >	
+%mathml-in-pubmed;
+
+
+		 
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "#PCDATA | b | i | sup | sub | u" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+<!ATTLIST       PubmedArticleSet
+>
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+<!ATTLIST       BookDocumentSet
+>
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+<!ATTLIST       PubmedBookArticleSet
+>
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+<!ATTLIST       PubmedArticle
+>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+<!ATTLIST       PubmedBookArticle
+>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, CitationString?, GrantList?, ItemList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText   (%text; | mml:math | DispFormula)* >
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation  (%text;)*>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle   (%text; | mml:math)*>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		(%text;)*> <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle        (%text; | mml:math)*>
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	CitationString     (%text;)*>
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement   (%text;)*>
+
+<!ELEMENT	CollectionTitle        (%text; | mml:math)*>
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName (%text;)*>
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | AssociatedPublication | CommentOn | CommentIn | ErratumIn | 
+		             ErratumFor | ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedFrom | RepublishedIn | 
+		             RetractionOf | RetractionIn | UpdateIn | UpdateOf | SummaryForPatientsIn | 
+		             OriginalReportIn | ReprintOf | ReprintIn | Cites)      #REQUIRED    >
+		             
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT       DispFormula     (mml:math) >
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		(%text;)*> <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword     (%text; | mml:math)*>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param  (%text;)*>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName     (%text;)*>
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	(%text;)*>
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	(%text;)*> <!-- subscript -->
+
+<!ELEMENT	Suffix (%text;)*>
+
+<!ELEMENT	sup	(%text;)*> <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type (Disease | Protocol | Organism) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		(%text;)*> <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle     (%text; | mml:math)*>
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle (%text;)*>
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_190101.dtd

@@ -0,0 +1,478 @@
+<!--
+
+2018-09-01
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd
+
+Additions/Changes since 180601 DTD: 
+
+	1.  Added elements to capture reference citations:
+			<ReferenceList>
+			<Reference>
+			<Citation>
+	2.  Removed <CitationString> from book records.
+	3. Added four values to CommentsCorrections/@RefType
+	       CorrectedandRepublishedIn
+	       CorrectedandRepublishedFrom
+	       RetractedandRepublishedIn
+	       RetractedandRepublishedFrom
+	4. Added "plain-language-summary" to allowed values for @Type on 
+	    <OtherAbstract>
+
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE:  StartPage and EndPage in Pagination element are not currently used; are 
+	reserved for future use. 
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+       
+<!-- ============================================================= -->
+<!--                     MATHML 3.0 SETUP                        -->
+<!-- ============================================================= -->
+<!--                    MATHML SETUP FILE                 -->
+<!ENTITY % mathml-in-pubmed     SYSTEM        "mathml-in-pubmed.mod"               >	
+%mathml-in-pubmed;
+
+
+		 
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "#PCDATA | b | i | sup | sub | u" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+<!ATTLIST       PubmedArticleSet
+>
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+<!ATTLIST       BookDocumentSet
+>
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+<!ATTLIST       PubmedBookArticleSet
+>
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+<!ATTLIST       PubmedArticle
+>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+<!ATTLIST       PubmedBookArticle
+>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, GrantList?, ItemList*, ReferenceList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?, ReferenceList*) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText   (%text; | mml:math | DispFormula)* >
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation  (%text;)*>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle   (%text; | mml:math)*>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		(%text;)*> <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle        (%text; | mml:math)*>
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	Citation       (%text; | mml:math)*>
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement   (%text;)*>
+
+<!ELEMENT	CollectionTitle        (%text; | mml:math)*>
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName (%text;)*>
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | 
+		             AssociatedPublication | 
+		             CommentIn | CommentOn | 
+		             CorrectedandRepublishedIn | CorrectedandRepublishedFrom |
+		             ErratumIn | ErratumFor | 
+		             ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedIn | RepublishedFrom |  
+		             RetractedandRepublishedIn | RetractedandRepublishedFrom |
+		             RetractionIn | RetractionOf |  
+		             UpdateIn | UpdateOf | 
+		             SummaryForPatientsIn | 
+		             OriginalReportIn | 
+		             ReprintIn | ReprintOf |  
+		             Cites)      #REQUIRED    >
+		             
+
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT       DispFormula     (mml:math) >
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		(%text;)*> <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword     (%text; | mml:math)*>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher | 
+		    plain-language-summary) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param  (%text;)*>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName     (%text;)*>
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+
+<!ELEMENT	Reference (Citation, ArticleIdList?) >
+
+<!ELEMENT	ReferenceList (Title?, Reference*, ReferenceList*) >
+
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	(%text;)*>
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	(%text;)*> <!-- subscript -->
+
+<!ELEMENT	Suffix (%text;)*>
+
+<!ELEMENT	sup	(%text;)*> <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type (Disease | Protocol | Organism) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		(%text;)*> <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle     (%text; | mml:math)*>
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle (%text;)*>
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_230101.dtd

@@ -0,0 +1,468 @@
+<!--
+
+2022-12-06
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_230101.dtd
+
+Additions/Changes since pubmed_190101 DTD: 
+
+	1.  added values "Population" and "Anatomy" to a list of allowed values 
+	     of "Type" attribute of "SupplMeshName".
+
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE: The updated PubMed API now allows for the use of the StartPage and 
+	EndPage elements in Pagination.
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+       
+<!-- ============================================================= -->
+<!--                     MATHML 3.0 SETUP                        -->
+<!-- ============================================================= -->
+<!--                    MATHML SETUP FILE                 -->
+<!ENTITY % mathml-in-pubmed     SYSTEM        "mathml-in-pubmed.mod"               >	
+%mathml-in-pubmed;
+
+
+		 
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "#PCDATA | b | i | sup | sub | u" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+<!ATTLIST       PubmedArticleSet
+>
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+<!ATTLIST       BookDocumentSet
+>
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+<!ATTLIST       PubmedBookArticleSet
+>
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+<!ATTLIST       PubmedArticle
+>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+<!ATTLIST       PubmedBookArticle
+>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, GrantList?, ItemList*, ReferenceList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList?, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?, ReferenceList*) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText   (%text; | mml:math | DispFormula)* >
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation  (%text;)*>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle   (%text; | mml:math)*>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		(%text;)*> <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle        (%text; | mml:math)*>
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	Citation       (%text; | mml:math)*>
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement   (%text;)*>
+
+<!ELEMENT	CollectionTitle        (%text; | mml:math)*>
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName (%text;)*>
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | 
+		             AssociatedPublication | 
+		             CommentIn | CommentOn | 
+		             CorrectedandRepublishedIn | CorrectedandRepublishedFrom |
+		             ErratumIn | ErratumFor | 
+		             ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedIn | RepublishedFrom |  
+		             RetractedandRepublishedIn | RetractedandRepublishedFrom |
+		             RetractionIn | RetractionOf |  
+		             UpdateIn | UpdateOf | 
+		             SummaryForPatientsIn | 
+		             OriginalReportIn | 
+		             ReprintIn | ReprintOf |  
+		             Cites)      #REQUIRED    >
+		             
+
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT       DispFormula     (mml:math) >
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		(%text;)*> <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword     (%text; | mml:math)*>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher | 
+		    plain-language-summary) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param  (%text;)*>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName     (%text;)*>
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+
+<!ELEMENT	Reference (Citation, ArticleIdList?) >
+
+<!ELEMENT	ReferenceList (Title?, Reference*, ReferenceList*) >
+
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	(%text;)*>
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	(%text;)*> <!-- subscript -->
+
+<!ELEMENT	Suffix (%text;)*>
+
+<!ELEMENT	sup	(%text;)*> <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type ( Disease | Protocol | Organism | Anatomy | Population ) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		(%text;)*> <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle     (%text; | mml:math)*>
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle (%text;)*>
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_240101.dtd

@@ -0,0 +1,477 @@
+<!--
+
+2023-08-01
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_230101.dtd
+
+Additions/Changes since pubmed_230101 DTD: 
+
+	1. Updated model of "Grant" to make "Country" optional (0 or 1)
+	
+	2.  Added linking between group author names and investigator lists
+	   - allowed "InvestigatorList" to repeat in "MedlineCitation"
+	   - added "Investigators" attribute to "CollectiveName"
+	   - added "ID" attribute on "InvestigatorList"
+	
+	
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE: The updated PubMed API now allows for the use of the StartPage and 
+	EndPage elements in Pagination.
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+       
+<!-- ============================================================= -->
+<!--                     MATHML 3.0 SETUP                        -->
+<!-- ============================================================= -->
+<!--                    MATHML SETUP FILE                 -->
+<!ENTITY % mathml-in-pubmed     SYSTEM        "mathml-in-pubmed.mod"               >	
+%mathml-in-pubmed;
+
+
+		 
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "#PCDATA | b | i | sup | sub | u" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+<!ATTLIST       PubmedArticleSet
+>
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+<!ATTLIST       BookDocumentSet
+>
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+<!ATTLIST       PubmedBookArticleSet
+>
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+<!ATTLIST       PubmedArticle
+>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+<!ATTLIST       PubmedBookArticle
+>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, GrantList?, ItemList*, ReferenceList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList*, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?, ReferenceList*) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText   (%text; | mml:math | DispFormula)* >
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation  (%text;)*>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle   (%text; | mml:math)*>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		(%text;)*> <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle        (%text; | mml:math)*>
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	Citation       (%text; | mml:math)*>
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement   (%text;)*>
+
+<!ELEMENT	CollectionTitle        (%text; | mml:math)*>
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName (%text;)*>
+<!ATTLIST	CollectiveName
+                Investigators   IDREF   #IMPLIED>
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | 
+		             AssociatedPublication | 
+		             CommentIn | CommentOn | 
+		             CorrectedandRepublishedIn | CorrectedandRepublishedFrom |
+		             ErratumIn | ErratumFor | 
+		             ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedIn | RepublishedFrom |  
+		             RetractedandRepublishedIn | RetractedandRepublishedFrom |
+		             RetractionIn | RetractionOf |  
+		             UpdateIn | UpdateOf | 
+		             SummaryForPatientsIn | 
+		             OriginalReportIn | 
+		             ReprintIn | ReprintOf |  
+		             Cites)      #REQUIRED    >
+		             
+
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT       DispFormula     (mml:math) >
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country?)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		(%text;)*> <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+<!ATTLIST	InvestigatorList
+                ID  ID  #IMPLIED>
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword     (%text; | mml:math)*>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher | 
+		    plain-language-summary) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param  (%text;)*>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName     (%text;)*>
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+
+<!ELEMENT	Reference (Citation, ArticleIdList?) >
+
+<!ELEMENT	ReferenceList (Title?, Reference*, ReferenceList*) >
+
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	(%text;)*>
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	(%text;)*> <!-- subscript -->
+
+<!ELEMENT	Suffix (%text;)*>
+
+<!ELEMENT	sup	(%text;)*> <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type ( Disease | Protocol | Organism | Anatomy | Population ) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		(%text;)*> <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle     (%text; | mml:math)*>
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle (%text;)*>
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/pubmed_250101.dtd

@@ -0,0 +1,475 @@
+<!--
+
+2024-08-28
+
+This DTD supports both the E-utilities and ftp service data dissemination methods. 
+It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_230101.dtd
+
+Additions/Changes since pubmed_240101 DTD: 
+
+	1. Added AutoHM attribute to DescriptorName and QualifierName
+	
+	
+	
+	NOTE:  The use of "Medline" in a DTD or element name does not mean the record
+	represents a citation from a MEDLINE-selected journal.  When the NLM DTDs and
+	XML elements were first created, MEDLINE records were the only data exported.
+	Now NLM exports citations other than MEDLINE records using these tools. To
+	minimize unnecessary disruption to users of the data and tools, NLM has
+	retained the original DTD and element names (e.g., MedlineTA, MedlineJournalInfo). 
+ 
+	NOTE: The updated PubMed API now allows for the use of the StartPage and 
+	EndPage elements in Pagination.
+
+	* = 0 or more occurrences (optional element, repeatable)
+	? = 0 or 1 occurrences (optional element, at most 1)
+	+ = 1 or more occurrences (required element, repeatable)
+	| = choice, one or the other but not both
+	no symbol = required element
+
+       -->
+       
+<!-- ============================================================= -->
+<!--                     MATHML 3.0 SETUP                        -->
+<!-- ============================================================= -->
+<!--                    MATHML SETUP FILE                 -->
+<!ENTITY % mathml-in-pubmed     SYSTEM        "mathml-in-pubmed.mod"               >	
+%mathml-in-pubmed;
+
+
+		 
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+<!ENTITY % text             "#PCDATA | b | i | sup | sub | u" >
+
+ <!ENTITY % booklinkatts
+			 "book		CDATA			#IMPLIED
+			 part		CDATA			#IMPLIED
+			sec		CDATA			#IMPLIED"  >
+<!-- ================================================================= -->
+<!-- ================================================================= -->
+
+<!--  ================= Set-level elements ============================-->
+<!ELEMENT	PubmedArticleSet ((PubmedArticle | PubmedBookArticle)+, DeleteCitation?) >
+<!ATTLIST       PubmedArticleSet
+>
+
+<!ELEMENT	BookDocumentSet (BookDocument*, DeleteDocument?) >
+<!ATTLIST       BookDocumentSet
+>
+
+<!ELEMENT	PubmedBookArticleSet (PubmedBookArticle*)>
+<!ATTLIST       PubmedBookArticleSet
+>
+
+
+<!--  ============= Document-level elements ============================-->
+<!ELEMENT	PubmedArticle (MedlineCitation, PubmedData?)>
+<!ATTLIST       PubmedArticle
+>
+
+<!ELEMENT	PubmedBookArticle (BookDocument, PubmedBookData?)>
+<!ATTLIST       PubmedBookArticle
+>
+
+<!ELEMENT	BookDocument ( PMID, ArticleIdList, Book, LocationLabel*, ArticleTitle?, VernacularTitle?,
+	Pagination?, Language*, AuthorList*, InvestigatorList?, PublicationType*, Abstract?, Sections?, KeywordList*, 
+	ContributionDate?, DateRevised?, GrantList?, ItemList*, ReferenceList*) >
+
+<!ELEMENT	DeleteCitation (PMID+) >
+
+<!ELEMENT	DeleteDocument (PMID*) >
+
+
+<!--  =============== Sub-Document wrapper elements =====================-->
+<!ELEMENT	MedlineCitation (PMID, DateCompleted?, DateRevised?, Article, 
+                             MedlineJournalInfo, ChemicalList?, SupplMeshList?,CitationSubset*, 
+                             CommentsCorrectionsList?, GeneSymbolList?, MeshHeadingList?, 
+                             NumberOfReferences?, PersonalNameSubjectList?, OtherID*, OtherAbstract*, 
+                             KeywordList*, CoiStatement?, SpaceFlightMission*, InvestigatorList*, GeneralNote*)>
+<!ATTLIST	MedlineCitation 
+		Owner  (NLM | NASA | PIP | KIE | HSR | HMD | NOTNLM) "NLM"
+		Status (Completed | In-Process | PubMed-not-MEDLINE |  In-Data-Review | Publisher | 
+		        MEDLINE | OLDMEDLINE) #REQUIRED 
+		VersionID CDATA #IMPLIED
+		VersionDate CDATA #IMPLIED 
+		IndexingMethod    CDATA  #IMPLIED >
+
+<!ELEMENT	PubmedData (History?, PublicationStatus, ArticleIdList, ObjectList?, ReferenceList*) >
+
+<!ELEMENT	PubmedBookData (History?, PublicationStatus, ArticleIdList, ObjectList?)>
+
+<!ELEMENT	Article (Journal,ArticleTitle,((Pagination, ELocationID*) | ELocationID+),
+                     Abstract?,AuthorList?, Language+, DataBankList?, GrantList?,
+                     PublicationTypeList, VernacularTitle?, ArticleDate*) >
+<!ATTLIST	Article 
+		    PubModel (Print | Print-Electronic | Electronic | Electronic-Print | Electronic-eCollection) #REQUIRED >
+		
+
+
+
+<!-- ================================================================= -->
+<!--  Everything else in alphabetical order                            -->
+<!-- ================================================================= -->
+
+<!ELEMENT	Abstract (AbstractText+, CopyrightInformation?)>
+
+<!ELEMENT	AbstractText   (%text; | mml:math | DispFormula)* >
+<!ATTLIST	AbstractText
+		    Label CDATA #IMPLIED
+		    NlmCategory (BACKGROUND | OBJECTIVE | METHODS | RESULTS | CONCLUSIONS | UNASSIGNED) #IMPLIED >
+		
+<!ELEMENT	AccessionNumber (#PCDATA) >
+
+<!ELEMENT	AccessionNumberList (AccessionNumber+) >
+
+<!ELEMENT	Acronym (#PCDATA) >
+
+<!ELEMENT	Affiliation  (%text;)*>
+
+<!ELEMENT	AffiliationInfo (Affiliation, Identifier*)>
+
+<!ELEMENT	Agency (#PCDATA) >
+
+<!ELEMENT	ArticleDate (Year, Month, Day) >
+<!ATTLIST	ArticleDate 
+            DateType CDATA  #FIXED "Electronic" >
+ 
+<!ELEMENT	ArticleId (#PCDATA) >
+<!ATTLIST   ArticleId
+	        IdType (doi | pii | pmcpid | pmpid | pmc | mid |
+                   sici | pubmed | medline | pmcid | pmcbook | bookaccession) "pubmed" >
+	      
+ <!ELEMENT	ArticleIdList (ArticleId+)>
+
+<!ELEMENT	ArticleTitle   (%text; | mml:math)*>
+<!ATTLIST   ArticleTitle	%booklinkatts; >
+
+<!ELEMENT	Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName), Identifier*, AffiliationInfo*) >
+<!ATTLIST	Author 
+            ValidYN (Y | N) "Y" 
+            EqualContrib    (Y | N)  #IMPLIED >
+            
+<!ELEMENT	AuthorList (Author+) >
+<!ATTLIST	AuthorList 
+            CompleteYN (Y | N) "Y" 
+            Type ( authors | editors )  #IMPLIED >
+
+<!ELEMENT	b		(%text;)*> <!-- bold -->
+
+<!ELEMENT	BeginningDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	Book ( Publisher, BookTitle, PubDate, BeginningDate?, EndingDate?, AuthorList*, InvestigatorList?, Volume?, 
+                    VolumeTitle?, Edition?, CollectionTitle?, Isbn*, ELocationID*, Medium?, ReportNumber?) >
+
+<!ELEMENT	BookTitle        (%text; | mml:math)*>
+<!ATTLIST   BookTitle	%booklinkatts; >
+
+<!ELEMENT	Chemical (RegistryNumber, NameOfSubstance) >
+
+<!ELEMENT	ChemicalList (Chemical+) >
+
+<!ELEMENT	Citation       (%text; | mml:math)*>
+
+<!ELEMENT	CitationSubset (#PCDATA) >
+
+<!ELEMENT   CoiStatement   (%text;)*>
+
+<!ELEMENT	CollectionTitle        (%text; | mml:math)*>
+<!ATTLIST   CollectionTitle	%booklinkatts; >
+
+<!ELEMENT	CollectiveName (%text;)*>
+<!ATTLIST	CollectiveName
+                Investigators   IDREF   #IMPLIED>
+
+<!ELEMENT	CommentsCorrections (RefSource,PMID?,Note?) >
+<!ATTLIST	CommentsCorrections 
+		     RefType (AssociatedDataset | 
+		             AssociatedPublication | 
+		             CommentIn | CommentOn | 
+		             CorrectedandRepublishedIn | CorrectedandRepublishedFrom |
+		             ErratumIn | ErratumFor | 
+		             ExpressionOfConcernIn | ExpressionOfConcernFor | 
+		             RepublishedIn | RepublishedFrom |  
+		             RetractedandRepublishedIn | RetractedandRepublishedFrom |
+		             RetractionIn | RetractionOf |  
+		             UpdateIn | UpdateOf | 
+		             SummaryForPatientsIn | 
+		             OriginalReportIn | 
+		             ReprintIn | ReprintOf |  
+		             Cites)      #REQUIRED    >
+		             
+
+<!ELEMENT	CommentsCorrectionsList (CommentsCorrections+) >
+
+<!ELEMENT	ContractNumber (#PCDATA) >
+
+<!ELEMENT	ContributionDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	CopyrightInformation (#PCDATA) >
+
+<!ELEMENT	Country (#PCDATA) >
+
+<!ELEMENT	DataBank (DataBankName, AccessionNumberList?) >
+
+<!ELEMENT	DataBankList (DataBank+) >
+
+<!ATTLIST	DataBankList 
+            CompleteYN (Y | N) "Y" >
+            
+<!ELEMENT	DataBankName (#PCDATA) >
+
+<!ELEMENT	DateCompleted (Year,Month,Day) >
+
+<!ELEMENT	DateRevised (Year,Month,Day) >
+
+<!ELEMENT	Day (#PCDATA )>
+
+<!ELEMENT	DescriptorName (#PCDATA) >
+<!ATTLIST	DescriptorName 
+		    MajorTopicYN (Y | N) "N"
+		    AutoHM (Y) #IMPLIED
+			 Type (Geographic) #IMPLIED
+		     UI CDATA #REQUIRED >
+
+<!ELEMENT       DispFormula     (mml:math) >
+<!ELEMENT	Edition (#PCDATA) >
+
+<!ELEMENT	ELocationID (#PCDATA) >
+<!ATTLIST	ELocationID 
+            EIdType (doi | pii) #REQUIRED 
+		    ValidYN  (Y | N) "Y">
+
+<!ELEMENT	EndingDate ( Year, ((Month, Day?) | Season)? ) >
+
+<!ELEMENT	EndPage (#PCDATA) >
+
+<!ELEMENT	ForeName (#PCDATA) >
+
+<!ELEMENT	GeneSymbol (#PCDATA) >
+
+<!ELEMENT	GeneSymbolList (GeneSymbol+)>
+
+<!ELEMENT	GeneralNote (#PCDATA) >
+<!ATTLIST	GeneralNote
+		     Owner (NLM | NASA | PIP | KIE | HSR | HMD) "NLM" >
+		     
+<!ELEMENT	Grant (GrantID?, Acronym?, Agency, Country?)>
+
+<!ELEMENT	GrantID (#PCDATA) >
+
+<!ELEMENT	GrantList (Grant+)>
+<!ATTLIST	GrantList 
+            CompleteYN (Y | N) "Y">
+   
+<!ELEMENT	History (PubMedPubDate+) >
+
+<!ELEMENT	Hour (#PCDATA) >
+
+<!ELEMENT	i		(%text;)*> <!-- italic -->
+
+<!ELEMENT	Identifier (#PCDATA) >
+<!ATTLIST	Identifier 
+		    Source CDATA #REQUIRED >
+		    
+<!ELEMENT	Initials (#PCDATA) >
+
+<!ELEMENT	Investigator (LastName, ForeName?, Initials?, Suffix?, Identifier*, AffiliationInfo*) >
+<!ATTLIST	Investigator 
+		    ValidYN (Y | N) "Y" >
+		    
+<!ELEMENT	InvestigatorList (Investigator+) >
+<!ATTLIST	InvestigatorList
+                ID  ID  #IMPLIED>
+
+<!ELEMENT	Isbn (#PCDATA) >
+
+<!ELEMENT	ISOAbbreviation (#PCDATA) >
+
+<!ELEMENT	ISSN (#PCDATA) >
+<!ATTLIST	ISSN 
+		    IssnType  (Electronic | Print) #REQUIRED >
+		    
+<!ELEMENT	ISSNLinking (#PCDATA) >
+
+<!ELEMENT	Issue (#PCDATA) >
+<!ELEMENT	Item (#PCDATA)>
+
+<!ELEMENT	ItemList (Item+)>
+<!ATTLIST   ItemList 
+            ListType CDATA #REQUIRED>
+
+<!ELEMENT	Journal (ISSN?, JournalIssue, Title?, ISOAbbreviation?)>
+
+<!ELEMENT	JournalIssue (Volume?, Issue?, PubDate) >
+<!ATTLIST	JournalIssue 
+		    CitedMedium (Internet | Print) #REQUIRED >
+		    
+<!ELEMENT	Keyword     (%text; | mml:math)*>
+<!ATTLIST	Keyword 
+		    MajorTopicYN (Y | N) "N" >
+		    
+<!ELEMENT	KeywordList (Keyword+) >
+<!ATTLIST	KeywordList 
+		    Owner (NLM | NLM-AUTO | NASA | PIP | KIE | NOTNLM | HHS) "NLM" >
+		    
+<!ELEMENT	Language (#PCDATA) >
+
+<!ELEMENT	LastName (#PCDATA) >
+
+<!ELEMENT	LocationLabel		(#PCDATA)>
+<!ATTLIST   LocationLabel
+			Type  (part|chapter|section|appendix|figure|table|box)  #IMPLIED >
+
+<!ELEMENT	Medium (#PCDATA) >
+
+<!ELEMENT	MedlineDate (#PCDATA) >
+
+<!ELEMENT	MedlineJournalInfo (Country?, MedlineTA, NlmUniqueID?, ISSNLinking?) >
+
+<!ELEMENT	MedlinePgn (#PCDATA) >
+
+<!ELEMENT	MedlineTA (#PCDATA) >
+
+<!ELEMENT	MeshHeading (DescriptorName, QualifierName*)>
+
+<!ELEMENT	MeshHeadingList (MeshHeading+)>
+
+<!ELEMENT	Minute (#PCDATA) >
+
+<!ELEMENT	Month (#PCDATA) >
+
+<!ELEMENT	NameOfSubstance (#PCDATA) >
+<!ATTLIST	NameOfSubstance 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	NlmUniqueID (#PCDATA) >
+
+<!ELEMENT	Note (#PCDATA) >
+
+<!ELEMENT	NumberOfReferences (#PCDATA) >
+
+<!ELEMENT	Object (Param*)>
+<!ATTLIST	Object 
+          Type CDATA #REQUIRED >
+  
+<!ELEMENT	ObjectList (Object+) >
+
+<!ELEMENT	OtherAbstract (AbstractText+, CopyrightInformation?) >
+
+<!ATTLIST	OtherAbstract 
+		    Type (AAMC | AIDS | KIE | PIP | NASA | Publisher | 
+		    plain-language-summary) #REQUIRED
+		    Language CDATA "eng" >
+		    
+<!ELEMENT	OtherID (#PCDATA) >
+<!ATTLIST	OtherID 
+		    Source (NASA | KIE | PIP | POP | ARPL | CPC | IND | CPFH | CLML |
+		            NRCBL | NLM | QCIM) #REQUIRED >
+		            
+<!ELEMENT	PMID (#PCDATA) >
+<!ATTLIST	PMID 
+		    Version CDATA #REQUIRED >
+		    
+<!ELEMENT	Pagination ((StartPage, EndPage?, MedlinePgn?) | MedlinePgn) >
+
+<!ELEMENT	Param  (%text;)*>
+<!ATTLIST	Param 
+             Name CDATA #REQUIRED >
+          
+<!ELEMENT	PersonalNameSubject (LastName, ForeName?, Initials?, Suffix?) >
+
+<!ELEMENT	PersonalNameSubjectList (PersonalNameSubject+) >
+
+<!ELEMENT	PubDate ((Year, ((Month, Day?) | Season)?) | MedlineDate) >
+
+<!ELEMENT	PublicationStatus (#PCDATA) >
+
+<!ELEMENT	PublicationType (#PCDATA) >
+<!ATTLIST	PublicationType 
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	PublicationTypeList (PublicationType+) >
+
+<!ELEMENT   PubMedPubDate (Year, Month, Day, (Hour, (Minute, Second?)?)?)>
+<!ATTLIST   PubMedPubDate
+    	     PubStatus (received | accepted | epublish | 
+                      ppublish | revised | aheadofprint | 
+                      retracted | ecollection | pmc | pmcr | pubmed | pubmedr | 
+                      premedline | medline | medliner | entrez | pmc-release) #REQUIRED >
+
+<!ELEMENT	Publisher (PublisherName, PublisherLocation?) >
+
+<!ELEMENT	PublisherLocation (#PCDATA) >
+
+<!ELEMENT	PublisherName     (%text;)*>
+
+<!ELEMENT	QualifierName (#PCDATA) >
+<!ATTLIST	QualifierName 
+		    AutoHM (Y) #IMPLIED
+			 MajorTopicYN (Y | N) "N"
+		    UI CDATA #REQUIRED >
+
+<!ELEMENT	Reference (Citation, ArticleIdList?) >
+
+<!ELEMENT	ReferenceList (Title?, Reference*, ReferenceList*) >
+
+<!ELEMENT	RefSource (#PCDATA) >
+
+<!ELEMENT	RegistryNumber (#PCDATA) >
+
+<!ELEMENT	ReportNumber (#PCDATA) >
+
+<!ELEMENT	Season (#PCDATA) >
+
+<!ELEMENT	Second (#PCDATA) >
+
+
+<!ELEMENT	Section	(LocationLabel?, SectionTitle, Section*) >
+
+<!ELEMENT	Sections	(Section+) >
+
+<!ELEMENT	SectionTitle	(%text;)*>
+<!ATTLIST   SectionTitle	%booklinkatts; >
+
+<!ELEMENT	SpaceFlightMission (#PCDATA) >
+
+<!ELEMENT	StartPage (#PCDATA) >
+
+<!ELEMENT	sub	(%text;)*> <!-- subscript -->
+
+<!ELEMENT	Suffix (%text;)*>
+
+<!ELEMENT	sup	(%text;)*> <!-- superscript -->
+
+<!ELEMENT	SupplMeshList (SupplMeshName+)>
+
+<!ELEMENT	SupplMeshName (#PCDATA) >
+<!ATTLIST	SupplMeshName 
+		    Type ( Disease | Protocol | Organism | Anatomy | Population ) #REQUIRED
+		    UI CDATA #REQUIRED >
+		    
+<!ELEMENT	Title (#PCDATA) >
+
+<!ELEMENT	u		(%text;)*> <!-- underline -->                              
+
+<!ELEMENT	URL (#PCDATA) >
+<!ATTLIST	URL
+	      lang (AF|AR|AZ|BG|CS|DA|DE|EN|EL|ES|FA|FI|FR|HE|
+                            HU|HY|IN|IS|IT|IW|JA|KA|KO|LT|MK|ML|NL|NO|
+                            PL|PT|PS|RO|RU|SL|SK|SQ|SR|SV|SW|TH|TR|UK|
+                           VI|ZH) #IMPLIED
+	      Type ( FullText | Summary | fulltext | summary) #IMPLIED >
+	      
+<!ELEMENT	VernacularTitle     (%text; | mml:math)*>
+
+<!ELEMENT	Volume (#PCDATA) >
+
+<!ELEMENT	VolumeTitle (%text;)*>
+
+<!ELEMENT	Year (#PCDATA) >
+
+
+
+
+

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/references.ent

@@ -0,0 +1,726 @@
+<!-- ============================================================= -->
+<!--  MODULE:    Bibliographic Reference (Citation) Class Elements -->
+<!--  VERSION:   2.0                                               -->
+<!--  DATE:      August 2004                                       -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
+<!--                        TYPICAL INVOCATION                     -->
+<!--
+"-//NLM//DTD Archiving and Interchange DTD Suite Bibliographic Reference (Citation) Class Elements v2.0 20040830//EN"
+Delivered as file "references.ent"                                 -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!-- SYSTEM:     Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!-- PURPOSE:    Defines the bibliographic reference elements      -->
+<!--                                                               -->
+<!--                                                               -->
+<!-- CONTAINS:   1) Default definition of the references class     -->
+<!--             2) Parameter Entities for attribute lists         -->
+<!--             3) Models for the bibliographic reference         -->
+<!--                class elements in alphabetical order           -->
+<!--                                                               -->
+<!-- CREATED FOR:                                                  -->
+<!--             Digital archives and publishers who wish to       -->
+<!--             create a custom XML DTD for original markup of    -->
+<!--             journal literature, books, and related material,  -->
+<!--             or for archiving and transferring such material   -->
+<!--             between archives.                                 -->
+<!--                                                               -->
+<!--             This DTD is in the public domain. An organization -->
+<!--             that wishes to create its own DTD from the suite  -->
+<!--             may do so without permission from NLM.            -->
+<!--                                                               -->
+<!--             The suite has been set up to be extended using a  -->
+<!--             new DTD file and a new DTD-specific customization -->
+<!--             module to redefine the many Parameter Entities.   -->
+<!--             Do not modify the suite directly or redistribute  -->
+<!--             modified versions of the suite.                   -->
+<!--                                                               -->
+<!--             In the interest of maintaining consistency and    -->
+<!--             clarity for potential users, NLM requests:        -->
+<!--                                                               -->
+<!--             1. If you create a DTD from the Archiving and     -->
+<!--                Interchange DTD Suite and intend to stay       -->
+<!--                compatible with the suite, then please include -->
+<!--                the following statement as a comment in all of -->
+<!--                your DTD modules:                              -->
+<!--                   "Created from, and fully compatible with,   -->
+<!--                    the Archiving and Interchange DTD Suite."  -->
+<!--                                                               -->
+<!--             2. If you alter one or more modules of the suite, -->
+<!--                then please rename your version and all its    -->
+<!--                modules to avoid any confusion with the        -->
+<!--                original suite. Also, please include the       -->
+<!--                following statement as a comment in all your   -->
+<!--                DTD modules:                                   -->
+<!--                   "Based in part on, but not fully compatible -->
+<!--                    with, the Archiving and Interchange DTD    --> 
+<!--                    Suite."                                    -->
+<!--                                                               -->
+<!--             Suggestions for refinements and enhancements to   -->
+<!--             the DTD suite should be sent in email to:         -->
+<!--                 archive-dtd@ncbi.nlm.nih.gov                  -->
+<!--                                                               -->
+<!-- ORIGINAL CREATION DATE:                                       -->
+<!--             December 2002                                     -->
+<!--                                                               -->
+<!-- CREATED BY: Jeff Beck       (NCBI)                            -->
+<!--             Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
+<!--             Bruce Rosenblum (Inera Inc.)                      -->
+<!--                                                               -->
+<!--             NLM thanks the Harvard University Libraries, both -->
+<!--             for proposing that a draft archiving NLM DTD for  --> 
+<!--             life sciences journals be extended to accommodate -->
+<!--             journals in all disciplines and for sponsoring    -->
+<!--             Bruce Rosenblum's collaboration with other DTD    -->
+<!--             authors in completing Version 1.0. The Andrew W.  --> 
+<!--             Mellon Foundation provided support for these      --> 
+<!--             important contributions.                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DTD VERSION/CHANGE HISTORY                 -->
+<!-- ============================================================= -->
+<!--
+
+     =============================================================
+
+Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)
+
+     =============================================================
+     Version 2.0                       (DAL/BTU) v2.0 (2004-08-30)
+     
+     Major requirement changes led to the new release, producing
+     DTD version "2.0":
+       a) The splitting of the Archival and Interchange Tag Set 
+          DTDs into three DTDs from two: an authoring DTD, an
+          archive regularization and interchange DTD (the
+          current Blue Publishing DTD), and a preservationist 
+          archive DTD (the current Green Archiving and Interchange 
+          DTD).
+       b) AIT Working Group suggestions from the June 04 meeting 
+          and June/July 2004 followup discussions
+       c) Suite remodularization to meet new (and newly articulated)
+          modularization requirements
+       d) New or renamed classes and mixes to make modifications
+          easier and more consistent
+
+ 12. COMPLETE MODELS WHEN OVER-RIDING A MODEL 
+     (for all Parameter Entities suffixed "-model")
+     ### Customization Alert ###
+     Added internal parentheses to Parameter Entity and removed 
+     them from Element Declaration for:
+     - %note-model;
+     - %ref-list-model;
+     - %ref-model;
+     - and removed the parentheses for <person-group>
+
+ 11. DEFAULT CLASSES - Were moved from this module to 
+     %default-classes.ent;
+
+ 10. REFERENCES.CLASS - Added the following elements to the
+     %references.class;:
+      - <issue-id>
+      - <issue-title>
+      - <page-range>
+      - <role>
+      - <string-name>
+      - <volume-id>
+
+  9. EMAIL AND URI
+     a. Added to %source-elements; by changing 
+         %ext-links.class; ==> %address-link.class;
+
+  8. LOOSENING ELEMENT USAGE in Archiving DTD and Suite
+     a. Rewrote content model for access-date as a new Parameter
+        Entity %access-date-elements;
+     b. Allowed all date components (%date-part.class;)
+        inside this PE in Archiving DTD (Green) customization
+     c. The default value is the empty string in this module,
+        therefore, access date, by default, contains nothing 
+        but #PCDATA.
+
+  7. ROLE ELEMENT - Was added to the default references class 
+     %references.class;
+
+  6. PERSON GROUP - To add <string-name> as well as correct various
+     classing problems:
+
+     a. Content model was made into a Parameter Entity
+        %person-group-model;
+
+     b. The content model was changed to incorporate the new
+         -%name.class;, which adds both <string-name> and <collab>
+
+  5. NAME CLASS / STRING NAME
+     a. Created a new element <string-name> for names that
+        do not follow the former, strict personal name model.
+
+     b. Created a new class %name.class; to hold all the ways
+        to name people: <name>, <string-name>, and <collab>
+        who produce products or articles. Used in:
+        - <person-group>
+     
+     c. To allow <string-name> to be used anywhere <name> is
+        used:
+        - Added to default %references.class;
+
+  4. NEW PARAMETER ENTITIES - To correct potential classing 
+     problems, created the following new Parameter Entities:
+     a. NEW CLASSES
+        - %just-para.class; used in <annotation>, -%note-model;
+        - %ref-list.class; used in <ref-list>
+     b. NEW MIXES 
+        - <edition>       -%edition-elements;
+        - <gov>           -%gov-elements;
+        - <patent>        -%patent-elements;
+        - <series-title>  -%series-title-elements;
+        - <std>           -%std-elements;
+        - <time-stamp>    -%time-stamp-elements;
+
+
+  3. Updated public identifier to "v2.0 20040830"         
+     
+     =============================================================
+     Version 1.1                           (TRG) v1.1 (2003-11-01)
+
+  2. Added element <page-count> to parameter entity 
+     %references.class;
+     Rationale:  Permit tagging of page count where included in
+     references.
+
+     =============================================================
+     Version 1.0 Post Publishing DTD Change (DAL) v 1.0 2003-02-10
+
+  1. Removed <other-ref>, since the Publishing (authoring) DTD did
+     not need it and that is what it had been made for. It was 
+     never to be used for conversion or interchange, so it's gone.
+     Removed %other-ref-elements; as well. It did not need to be 
+     removed from any context, as it was never used.
+                                                                   -->
+                                                                   
+                                                                   
+<!-- ============================================================= -->
+<!--                    PARAMETER ENTITY DEPENDENCIES             
+                        Requires the following parameter entities
+                        be defined before calling this module, 
+                        usually accomplished in the Customization
+                        Module for the specific DTD:
+                          - %emphasis.class;
+                          - %just-rendition;
+                          - %label.class;
+                          - %para-level;
+                          - %rendition-plus;
+                          - %simple-phrase;
+                          - %subsup.class;                         -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    PARAMETER ENTITIES FOR ATTRIBUTE LISTS     -->
+<!-- ============================================================= -->
+                                                                
+                                                                 
+<!--                    PERSON GROUP ATTRIBUTES                    -->
+<!--                    Attributes for the <person-group> element  -->
+<!ENTITY %  person-group-atts  
+             "person-group-type 
+                        CDATA                             #IMPLIED"  >
+                                                                
+                                                                 
+<!--                    PUBLICATION IDENTIFIER ATTRIBUTES          -->
+<!--                    Attributes for the <pub-id> element        -->
+<!ENTITY %  pub-id-atts  
+             "pub-id-type 
+                        (%pub-id-types;)                  #IMPLIED"  >
+
+
+<!--         xml:lang   The language in which the value of the
+                        element is expressed.  Recommended best 
+                        practice is to use values as defined in
+                        RFC 1766, typically 2-letter language
+                        codes such as "FR" (French), "EN" (English),
+                        and "DE" (German). These values are NOT
+                        case sensitive, so "EN" = "en". The values
+                        may include hyphenated differentiations such 
+                        as "EN-AU" (Australian English) and "EN-US"
+                        (United States English).                   -->
+                                                                
+                                                                 
+<!--                    SOURCE ATTRIBUTES                          -->
+<!--                    Attributes for the <source> and 
+                        <trans-source> elements                    -->
+<!ENTITY %  source-atts
+             "xml:lang   NMTOKEN                           #IMPLIED" > 
+                                                                   
+<!-- ============================================================= -->
+<!--                    BIBLIOGRAPHIC REFERENCE LIST ELEMENTS      -->
+<!-- ============================================================= -->
+
+
+<!--ELEM   article-title       
+                        Defined in %common.ent;                    -->
+<!--ELEM   collab       Defined in %common.ent;                    -->
+<!--ELEM   conf-date    Defined in %common.ent;                    -->
+<!--ELEM   conf-loc     Defined in %common.ent;                    -->
+<!--ELEM   conf-name    Defined in %common.ent;                    -->
+<!--ELEM   day          Defined in %common.ent;                    -->
+<!--ELEM   elocation-id Defined in %common.ent;                    -->
+<!--ELEM   email        Defined in %common.ent;                    -->
+<!--ELEM   fpage        Defined in %common.ent;                    -->
+<!--ELEM   issn         Defined in %common.ent;                    -->
+<!--ELEM   issue        Defined in %common.ent;                    -->
+<!--ELEM   lpage        Defined in %common.ent;                    -->
+<!--ELEM   month        Defined in %common.ent;                    -->
+<!--ELEM   publisher-loc       
+                        Defined in %common.ent;                    -->
+<!--ELEM   publisher-name      
+                        Defined in %common.ent;                    -->
+<!--ELEM   season       Defined in %common.ent;                    -->
+<!--ELEM   title        Defined in %common.ent;                    -->
+<!--ELEM   trans-title  Defined in %common.ent;                    -->
+<!--ELEM   volume       Defined in %common.ent;                    -->
+<!--ELEM   year         Defined in %common.ent;                    -->
+
+
+<!--                    REFERENCE LIST MODEL                       -->
+<!--                    Content model for the <ref-list> element   -->
+<!ENTITY % ref-list-model
+                        "(title?, (%para-level;)*, ref*, 
+                         (%ref-list.class;)* )"                      > 
+
+
+<!--                    REFERENCE LIST (BIBLIOGRAPHIC REFERENCE LIST)
+                                                                   -->
+<!--                    List of references (citations) for the
+                        article.  Often called "References", 
+                        "Bibliography", or "Additional Reading". No
+                        distinction is made between lists of cited
+                        references and lists of suggested references.
+                        Authoring Note: The optional paragraph-level
+                        elements after the title allow for those rare
+                        cases where there is explanatory material
+                        inside the list, before the references. There
+                        may also be similar explanatory material 
+                        inside each reference group. Explanatory
+                        material preceding a citation will need to
+                        be placed inside the citation.             -->
+<!ELEMENT  ref-list     %ref-list-model;                             >
+
+
+<!--                    REFERENCE ITEM MODEL                       -->
+<!--                    Content model for the <ref> element        -->
+<!ENTITY % ref-model    "(label?, (citation | note)+ )"              > 
+
+
+<!--                    REFERENCE ITEM                             -->
+<!--                    One item in a bibliographic list, typically
+                        a citation describing a referenced work, but
+                        some journals may place notes in this list as
+                        well as citations.
+                        Conversion Note: There is usually a number or
+                        other label preceding each citation, which 
+                        the tagger may choose to preserve using the 
+                        label attribute.                           -->
+<!ELEMENT  ref          %ref-model;                                  >
+<!--         id         Unique identifier so that citation can be
+                        referenced                                 -->
+<!ATTLIST  ref
+             id         ID                                 #IMPLIED  >
+
+
+<!--ELEM   citation     Defined in %common.ent;                    -->
+
+
+<!--                    NOTE IN A REFERENCE LIST MODEL             -->
+<!ENTITY % note-model   "(label?, (%just-para.class;)+ )"            > 
+
+
+<!--                    NOTE IN A REFERENCE LIST                   -->
+<!--                    Used to tag non-citation material that 
+                        sometimes within a reference list, for 
+                        example, used to tag end note material when 
+                        such a note is placed within a reference 
+                        list.
+                        Authoring Note: For conversion use only. For
+                        creating new reference lists, notes should
+                        not be intermingled with citations.        -->
+<!ELEMENT  note         %note-model;                                 > 
+<!--         id         Unique identifier so that citation can be
+                        referenced                                 -->
+<!ATTLIST  note
+             id         ID                                 #IMPLIED  >
+
+
+<!-- ============================================================= -->
+<!--                    BIBLIOGRAPHIC REFERENCE CLASS              -->
+<!-- ============================================================= -->
+
+
+<!--                    ACCESS DATE ELEMENTS                       -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        the Access Date <access-date> element      -->
+<!ENTITY % access-date-elements 
+                        " "                                          >
+
+
+<!--                    ACCESS DATE FOR CITED WORK                 -->
+<!--                    The date on which the work which is cited
+                        was examined. Some online resources are 
+                        changing so quickly that a citation to the 
+                        resource is not complete without the date 
+                        on which the cited resource was examined, 
+                        since a day before or a day later the 
+                        relevant material might be different.
+                        Related Elements: The related element
+                        <time-stamp> is used to record not the time 
+                        when a cited resource was examined, but the
+                        time stamp that was found on the resource
+                        when it was examined, for time-stamped
+                        resources.                                 -->
+<!ELEMENT  access-date  (#PCDATA %access-date-elements;)*            >
+
+
+<!--                    ANNOTATION IN A CITATION                   -->
+<!--                    Most citations just provide the bibliographic
+                        information for a cited reference but a few
+                        describe or comment upon the nature or
+                        quality of the reference or summarize its
+                        findings.
+                        Display Note: All of the other reference
+                        elements are inline elements. In contrast,
+                        an Annotation may be considered a block
+                        element, with space before it and after it.-->
+<!ELEMENT  annotation   ((%just-para.class;)+)                       >
+
+
+<!--                    COMMENT ELEMENTS                           -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        the Comment in a Citation <comment> element.
+                        DESIGN NOTE: All inline mixes begin with an
+                        OR bar, but since %simple-phrase; is an 
+                        inline mix, the OR bar is already there.   -->
+<!ENTITY % comment-elements 
+                        "%simple-phrase;"                            >
+
+
+<!--                    COMMENT IN A CITATION                      -->
+<!--                    Used to mark unstructured text within an
+                        otherwise element structured reference.
+                        In an unstructured reference, this text would
+                        merely be data characters.
+                        Typical comments could include:
+                          <comment>[Abstract]</comment>
+                          <comment> translated from Russian</comment>
+                        DESIGN NOTE: The <comment> element is defined
+                        here largely for the sake of conversion, to
+                        preserve the semantic markup when translating
+                        from other DTDs.
+                        Authoring and Conversion Note: The Comment
+                        element should be used to mark substantive
+                        text only; it should NOT be used to markup
+                        punctuation that occurs between elements.
+                        Display Note: Comments should appear inline
+                        with other reference elements.  This is a
+                        very different rendering from that given the
+                        similar element Annotation, which is
+                        typically a longer commentary concerning a
+                        citation that is rendered as a block
+                        element.
+                        DESIGN NOTE: All inline mixes begin with an
+                        OR bar, but since %simple-phrase; is an 
+                        inline mix, the OR bar is already there.   -->
+<!ELEMENT  comment      (#PCDATA %comment-elements;)*                >
+
+
+<!--                    EDITION ELEMENTS                           -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        <edition>                             
+                        Design Note: -%just-rendition; begins with
+                        an OR bar, so this inline mix begins with
+                        an OR bar.                                 -->
+<!ENTITY % edition-elements
+                        "%just-rendition;"                           >
+
+<!--                    EDITION, CITED                             -->
+<!--                    The edition number of a cited publication  -->
+<!ELEMENT  edition      (#PCDATA %edition-elements;)*                >
+
+
+<!--                    GOVERNMENT REPORT ELEMENTS                 -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        <gov>                             
+                        Design Note: -%rendition-plus; begins with
+                        an OR bar, so this inline mix begins with
+                        an OR bar.                                 -->
+<!ENTITY % gov-elements "%rendition-plus;"                           >
+
+
+<!--                    GOVERNMENT REPORT, CITED                   -->
+<!--                    The identification information (typically the
+                        title and/or an identification number) for 
+                        a cited governmental report or other 
+                        government publication                     -->
+<!ELEMENT  gov          (#PCDATA %gov-elements;)*                    >
+
+
+<!--                    ISBN                                       -->
+<!--                    International Standard Book Number         -->
+<!ELEMENT  isbn         (#PCDATA)                                    >
+
+
+<!--                    PATENT NUMBER ELEMENTS                     -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        <patent>                             
+                        Design Note: -%just-rendition; begins with
+                        an OR bar, so this inline mix begins with
+                        an OR bar.                                 -->
+<!ENTITY % patent-elements 
+                        "%just-rendition;"                           >
+
+
+<!--                    PATENT NUMBER, CITED                       -->
+<!--                    The identification information (typically the
+                        patent number or number and name) for a  
+                        cited patent                               -->
+<!ELEMENT  patent       (#PCDATA %patent-elements;)*                 >
+
+
+<!--                    PERSON GROUP MODEL                         -->
+<!--                    Content model for the Person Group element -->
+<!ENTITY % person-group-model
+                        "(%name.class; | aff | etal)*"               >
+
+
+<!--                    PERSON GROUP FOR A CITED PUBLICATION       -->
+<!--                    Wrapper element for one or more authors,
+                        editors, translators, etc. named in a cited
+                        reference.
+                        Remarks: Similar to the <contrib-group>
+                        element in the metadata, but could not use
+                        the same name (as this is a DTD not a schema)
+                        since the content is different.            -->
+<!ELEMENT  person-group %person-group-model;                         >
+<!--         person-group-type 
+                        Identifies the "role" of the persons being
+                        named, a group of authors, a group of 
+                        editors, members of the G&S chorus, etc.
+                        Valid Types include:
+                          author - Content creators
+                          editor - Content editors
+                          guest-editor 
+                                 - Content editor that has been 
+                                   invited to edit all or part of 
+                                   a work
+                          inventor 
+                                 - Idea, software, or machine creator
+                          assignee 
+                                 - Person to whom a patent is awarded
+                          translator
+                                 - Translated the cited work from 
+                                   one language into another
+                          trans-editor 
+                                 - Editor of a translated version of
+                                   a work
+                          all-authors
+                                 - Used to identify a complete list
+                                   of authors when a subset of the 
+                                   author group is used elsewhere 
+                                   in the citation. This may occur, 
+                                   for example, when a citation 
+                                   identifies both a book and a
+                                   chapter within the book.
+                          compiler
+                                 - Put together a composite work
+                                   from multiple sources
+                                                                   -->
+<!ATTLIST  person-group 
+             %person-group-atts;                                     >
+
+
+<!--                    PUBLICATION IDENTIFIER FOR A CITED PUBLICATION
+                                                                   -->
+<!--                    The identifier of a publication such as a
+                        related journal article that is listed 
+                        within a Citation <citation> inside the
+                        bibliographic reference list <ref-list> of 
+                        an article.                                -->
+<!ELEMENT  pub-id       (#PCDATA)                                    >
+<!--         pub-id-type 
+                        The "pub-id-type" attribute names the
+                        type of identifier, or the organization or 
+                        system that defined this identifier for the 
+                        identifier of the journal article or a 
+                        cited publication.
+                           Used on the <article-id> element, which 
+                        holds an identifier for the entire article.  
+                           Also used on the <pub-id> element, which 
+                        is an identifier for a publication cited in 
+                        a bibliographic reference (citation).
+                        Valid Types include:
+                          coden  - Obsolete PDB/CCDC identifier, may
+                                   be present on older articles
+                          doi    - Digital Object Identifier for
+                                   the publication being referenced
+                          medline- NLM Medline identifier
+                          other  - None of the named identifiers
+                          pii    - Publisher Item Identifier, see
+                                    /epub/piius.htm
+                          pmid   - PubMed ID (see
+                                   www.ncbi.nlm.nih.gov/entrez/
+                                   query.fcgi?db=PubMed)         
+                          publisher-id - 
+                                   Publisher's identifying number 
+                                   such as an 'article-id', 'artnum',
+                                   'identifier', 'article- number', 
+                                   etc.
+                          sici   - Serial Item and Contribution 
+                                   Identifier (SICI). A journal 
+                                   article may have more than one 
+                                   SICI, one for a print version and
+                                   one for an electronic version.  -->
+<!ATTLIST  pub-id  
+             %pub-id-atts;                                           >
+
+
+<!--                    SERIES ELEMENTS                            -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        <series>                             
+                        Design Note: -%rendition-plus; begins with
+                        an OR bar, so this inline mix begins with
+                        an OR bar.                                 -->
+<!ENTITY % series-elements "%rendition-plus;"                        >
+
+
+<!--                    SERIES                                     -->
+<!--                    Container element for any series information
+                        used in a citation. For example, within a
+                        citation to a non-journal item that spans
+                        multiple volumes, this element could contain
+                        the unique title of the entire series:
+                          <citation citation-type="book">
+                          <name>...</name> and <name>...</name>
+                          <year>1989</year>. <series>The Birds of
+                          South America</series>. <volume>1</volume>.
+                          <source>The Oscine Passerines</source>. 
+                          <publisher-name>University of Texas 
+                          Press</publisher-name>
+                          , <publisher-loc>Austin</publisher-loc>
+                          </citation>
+                                                                   -->
+<!ELEMENT  series       (#PCDATA %series-elements;)*                 >
+
+
+<!--                    STANDARD ELEMENTS                          -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        <std>                             
+                        Design Note: -%rendition-plus; begins with
+                        an OR bar, so this inline mix begins with
+                        an OR bar.                                 -->
+<!ENTITY % std-elements "%rendition-plus;"                           >
+
+
+<!--                    STANDARD, CITED                            -->
+<!--                    The identification information (typically the
+                        standard number, organization, and name) for 
+                        a cited standard, where "standard" is defined
+                        as a document produced by a recognized
+                        standards body such ISO, IEEE, OASIS, ANSI,
+                        etc.                                       -->
+<!ELEMENT  std          (#PCDATA %std-elements;)*                    >
+
+
+<!--                    SOURCE ELEMENTS                            -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        a <source>.                                -->
+<!ENTITY % source-elements
+                        "| %emphasis.class; | %address-link.class; |
+                         %subsup.class;"                             >
+
+
+<!--                    SOURCE                                     -->
+<!--                    Within a citation, this is the title of a
+                        journal, book, conference proceedings, etc.
+                        that is the source of the cited material.  -->
+<!ELEMENT  source       (#PCDATA %source-elements;)*                 >
+<!--         xml:lang   The language in which the value of the
+                        element is expressed.  Recommended best 
+                        practice is to use values as defined in
+                        RFC 1766, typically 2-letter language
+                        codes such as "FR" (French), "EN" (English),
+                        and "DE" (German). These values are NOT
+                        case sensitive, so "EN" = "en". The values
+                        may include hyphenated differentiations such 
+                        as "EN-AU" (Australian English) and "EN-US"
+                        (United States English).                   -->
+<!ATTLIST  source
+             %source-atts;                                           > 
+
+
+<!--                    TIME STAMP ELEMENTS                        -->
+<!--                    The elements that can be included along with
+                        data characters inside the content model of
+                        a <time-stamp>.                            -->
+<!ENTITY % time-stamp-elements
+                        " "                                          >
+
+
+<!--                    TIME STAMP FOR CITED WORK                 -->
+<!--                    Used to record any time stamp that was 
+                        found on the cited resource when it was 
+                        examined, for resources such as databases
+                        that may use a time signature to identify
+                        different versions. Note: This is not the 
+                        time when the cited resource was examined, 
+                        but rather the time it was produced,
+                        distributed, whatever milestone the resource
+                        creators chose to stamp time stamp.
+                        Related Element: <access-date> is the date 
+                        on which the cited work was examined. Some 
+                        online resources are changing so quickly 
+                        that a citation to the resource is not 
+                        complete without the date.                 -->
+<!ELEMENT  time-stamp   (#PCDATA %time-stamp-elements;)              >
+
+
+<!--                    TRANSLATED SOURCE                          -->
+<!--                    Within a citation, this is the title of a
+                        journal, book, conference proceedings, etc.
+                        that is the source of the cited material,
+                        but with the source name given in a different
+                        language from the source as given in the 
+                        <source> element. For example, if an article
+                        is originally in French, the <source> name
+                        would be the French name and the 
+                        <trans-source> might be in English.        -->
+<!ELEMENT  trans-source (#PCDATA %source-elements;)*                 >
+<!--         xml:lang   The language in which the value of the
+                        element is expressed.  Recommended best 
+                        practice is to use values as defined in
+                        RFC 1766, typically 2-letter language
+                        codes such as "FR" (French), "EN" (English),
+                        and "DE" (German). These values are NOT
+                        case sensitive, so "EN" = "en". The values
+                        may include hyphenated differentiates such 
+                        as "EN-AU" (Australian English) and "EN-US"
+                        (United States English).                   -->
+<!ATTLIST  trans-source
+             %source-atts;                                           > 
+
+
+<!-- ================== End Bibliographic Class Module =========== -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/section.ent

@@ -0,0 +1,220 @@
+<!-- ============================================================= -->
+<!--  MODULE:    Section Class Elements                            -->
+<!--  VERSION:   2.0                                               -->
+<!--  DATE:      August 2004                                       -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
+<!--                        TYPICAL INVOCATION                     -->
+<!--
+"-//NLM//DTD Archiving and Interchange DTD Suite Section Class Elements v2.0 20040830//EN"
+     Delivered as file "section.ent"                               -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!-- SYSTEM:     Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!-- PURPOSE:    Defines the member of the sec.class, that is,     -->
+<!--             names all section-level elements in the           -->
+<!--             Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!--             At the time of the initial DTD creation           -->
+<!--             there is only one such element, Section itself    -->
+<!--             <sec>, but future expansion to named sections     -->
+<!--             (such as <methodology> or <materials> or any      -->
+<!--             new section-level structures would be added here. -->
+<!--                                                               -->
+<!-- CONTAINS:   1) Default definition of the section class        -->
+<!--             2) Defaults for attribute lists                   -->
+<!--             3) Section <sec>                                  -->
+<!--                                                               -->
+<!-- CREATED FOR:                                                  -->
+<!--             Digital archives and publishers who wish to       -->
+<!--             create a custom XML DTD for original markup of    -->
+<!--             journal literature, books, and related material,  -->
+<!--             or for archiving and transferring such material   -->
+<!--             between archives.                                 -->
+<!--                                                               -->
+<!--             This DTD is in the public domain. An organization -->
+<!--             that wishes to create its own DTD from the suite  -->
+<!--             may do so without permission from NLM.            -->
+<!--                                                               -->
+<!--             The suite has been set up to be extended using a  -->
+<!--             new DTD file and a new DTD-specific customization -->
+<!--             module to redefine the many Parameter Entities.   -->
+<!--             Do not modify the suite directly or redistribute  -->
+<!--             modified versions of the suite.                   -->
+<!--                                                               -->
+<!--             In the interest of maintaining consistency and    -->
+<!--             clarity for potential users, NLM requests:        -->
+<!--                                                               -->
+<!--             1. If you create a DTD from the Archiving and     -->
+<!--                Interchange DTD Suite and intend to stay       -->
+<!--                compatible with the suite, then please include -->
+<!--                the following statement as a comment in all of -->
+<!--                your DTD modules:                              -->
+<!--                   "Created from, and fully compatible with,   -->
+<!--                    the Archiving and Interchange DTD Suite."  -->
+<!--                                                               -->
+<!--             2. If you alter one or more modules of the suite, -->
+<!--                then please rename your version and all its    -->
+<!--                modules to avoid any confusion with the        -->
+<!--                original suite. Also, please include the       -->
+<!--                following statement as a comment in all your   -->
+<!--                DTD modules:                                   -->
+<!--                   "Based in part on, but not fully compatible -->
+<!--                    with, the Archiving and Interchange DTD    --> 
+<!--                    Suite."                                    -->
+<!--                                                               -->
+<!--             Suggestions for refinements and enhancements to   -->
+<!--             the DTD suite should be sent in email to:         -->
+<!--                 archive-dtd@ncbi.nlm.nih.gov                  -->
+<!--                                                               -->
+<!-- ORIGINAL CREATION DATE:                                       -->
+<!--             December 2002                                     -->
+<!--                                                               -->
+<!-- CREATED BY: Jeff Beck       (NCBI)                            -->
+<!--             Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
+<!--             Bruce Rosenblum (Inera Inc.)                      -->
+<!--                                                               -->
+<!--             NLM thanks the Harvard University Libraries, both -->
+<!--             for proposing that a draft archiving NLM DTD for  --> 
+<!--             life sciences journals be extended to accommodate -->
+<!--             journals in all disciplines and for sponsoring    -->
+<!--             Bruce Rosenblum's collaboration with other DTD    -->
+<!--             authors in completing Version 1.0. The Andrew W.  --> 
+<!--             Mellon Foundation provided support for these      --> 
+<!--             important contributions.                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DTD VERSION/CHANGE HISTORY                 -->
+<!-- ============================================================= -->
+<!--
+     =============================================================
+
+Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)
+
+     =============================================================
+     Version 2.0                       (DAL/BTU) v2.0 (2004-08-30)
+     
+     Major requirement changes led to the new release, producing
+     DTD version "2.0":
+       a) The splitting of the Archival and Interchange Tag Set 
+          DTDs into three DTDs from two: an authoring DTD, an
+          archive regularization and interchange DTD (the
+          current Blue Publishing DTD), and a preservationist 
+          archive DTD (the current Green Archiving and Interchange 
+          DTD).
+       b) AIT Working Group suggestions from the June 04 meeting 
+          and June/July 2004 followup discussions
+       c) Suite remodularization to meet new (and newly articulated)
+          modularization requirements
+       d) New or renamed classes and mixes to make modifications
+          easier and more consistent
+
+  3. COMPLETE MODELS WHEN OVER-RIDING A MODEL 
+     (for all Parameter Entities suffixed "-model")
+     ### Customization Alert ###
+     Added internal parentheses to Parameter Entity and removed 
+     them from Element Declaration for:
+     - %sec-model;
+
+  2. DEFAULT CLASSES - Were moved from this module to 
+     %default-classes.ent;
+  
+  1. Updated public identifier to "v2.0 20040830"          
+                                                                   -->
+
+
+<!-- ============================================================= -->
+<!--                    PARAMETER ENTITY DEPENDENCIES             
+                        Requires the following parameter entities
+                        be defined before calling this module. 
+                        The content-model Parameter Entities are
+                        defined in %common.ent; but may be
+                        redefined in the Customization Module for
+                        the specific DTD:
+                          %sec-model; - Content model for section-like 
+                                        elements  
+                                                                   -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DEFAULTS FOR ATTRIBUTE LISTS               -->
+<!-- ============================================================= -->
+
+
+<!--                    SECTION ATTRIBUTES                         -->
+<!--                    Attribute list for Section element         -->
+<!ENTITY % sec-atts   
+            "id         ID                                 #IMPLIED
+             xml:lang   NMTOKEN                            #IMPLIED
+             sec-type   CDATA                              #IMPLIED 
+             disp-level CDATA                              #IMPLIED" >
+
+
+<!-- ============================================================= -->
+<!--                    SECTION ELEMENTS                           -->
+<!-- ============================================================= -->
+
+
+<!--                    SECTION                                    -->
+<!--                    A headed group of material; the basic 
+                        structural unit of the article             -->
+<!ELEMENT  sec          %sec-model;                                  >
+<!--         id         Unique identifier, so the Section can be
+                        referenced                   
+             xml:lang   The language in which the value of the
+                        element is expressed.  Recommended best 
+                        practice is to use values as defined in
+                        RFC 1766, typically 2-letter language
+                        codes such as "FR" (French), "EN" (English),
+                        and "DE" (German). These values are NOT
+                        case sensitive, so "EN" = "en". The values
+                        may include hyphenated differentiations such 
+                        as "EN-AU" (Australian English) and "EN-US"
+                        (United States English). 
+             sec-type   Conversion Note: This attribute may be used
+                        to retain information on the semantic
+                        content of a section where that is known.
+                        Authoring Note: Top-level sections (those 
+                        that are not nested inside other sections)
+                        may be assigned a "type" attribute for 
+                        indexing purposes. This attribute should be
+                        used only if the section is one of the listed
+                        types and should otherwise be omitted. A
+                        section that contains content of more than 
+                        one type should have the type IDs combined.
+                        (e.g., "Materials and Methods" would be
+                        type="materials|methods").  
+                        Types values are:         
+                          intro     Introduction/Synopsis
+                          materials Materials
+                          methods   Methods/Methodology/Procedures
+                          subjects  Patients/Participants/Subjects
+                          cases     Cases/Case Reports
+                          results   Results/Statement of Findings
+                          discussion  Discussion/Interpretation
+                          conclusions Conclusions/Comment
+             disp-level Sometimes in print or on screen, the display
+                        or apparent hierarchical level of a section
+                        is not the same as its real position in the
+                        hierarchy.  For example, in some styles,
+                        the "Clinical Finding" Section or the 
+                        'Methodology" Section always looks like a 
+                        particular level heading (say a level 2 head),
+                        wherever it falls in the hierarchy (say a 
+                        level 1 head or a level 3 head). This
+                        attribute can be used to record the needed
+                        display level. (Rare)                      -->
+<!ATTLIST  sec
+             %sec-atts;                                              >
+
+
+<!-- ================== End Section Class Module ================= -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/taxon.dtd

@@ -0,0 +1,131 @@
+<!-- ?xml version="1.0"? -->
+<!-- DOCTYPE TaxaSet PUBLIC "-//NLM//DTD TaxaSet, 20 February 2004//EN" "taxon.dtd" -->
+
+<!-- $Id: taxon.dtd 348960 2012-01-05 21:51:40Z yasmax $ -->
+
+<!-- ELEMENTS -->
+<!ELEMENT TaxId       (#PCDATA)>
+<!ELEMENT ParentTaxId (#PCDATA)>
+<!ELEMENT Division    (#PCDATA)>
+<!ELEMENT Rank        (#PCDATA)>
+<!ELEMENT ClassCDE    (#PCDATA)>
+<!ELEMENT DispName    (#PCDATA)>
+<!ELEMENT UniqueName  (#PCDATA)>
+<!ELEMENT GCId        (#PCDATA)>
+<!ELEMENT GCName      (#PCDATA)>
+<!ELEMENT MGCId       (#PCDATA)>
+<!ELEMENT MGCName     (#PCDATA)>
+<!ELEMENT Lineage     (#PCDATA)>
+<!ELEMENT PropName    (#PCDATA)>
+<!ELEMENT CreateDate  (#PCDATA)>
+<!ELEMENT UpdateDate  (#PCDATA)>
+<!ELEMENT PubDate     (#PCDATA)>
+<!ELEMENT CitId       (#PCDATA)>
+<!ELEMENT CitKey      (#PCDATA)>
+<!ELEMENT CitUrl      (#PCDATA)>
+<!ELEMENT CitText     (#PCDATA)>
+<!ELEMENT CitPubmedId (#PCDATA)>
+<!ELEMENT CitMedlineId (#PCDATA)>
+<!ELEMENT ModId       (#PCDATA)>
+<!ELEMENT ModType     (#PCDATA)>
+<!ELEMENT ModName     (#PCDATA)>
+<!ELEMENT ModGBhidden (#PCDATA)>
+<!ELEMENT RModId      (#PCDATA)>
+<!ELEMENT RTaxId      (#PCDATA)>
+<!ELEMENT ScientificName (#PCDATA)>
+<!ELEMENT GenbankCommonName (#PCDATA)>
+<!ELEMENT GenbankAcronym (#PCDATA)>
+<!ELEMENT BlastName   (#PCDATA)>
+<!ELEMENT EquivalentName   (#PCDATA)>
+<!ELEMENT Synonym     (#PCDATA)>
+<!ELEMENT Acronym     (#PCDATA)>
+<!ELEMENT Misspelling (#PCDATA)>
+<!ELEMENT Anamorph    (#PCDATA)>
+<!ELEMENT Includes    (#PCDATA)>
+<!ELEMENT CommonName  (#PCDATA)>
+<!ELEMENT Inpart      (#PCDATA)>
+<!ELEMENT Misnomer    (#PCDATA)>
+<!ELEMENT Teleomorph  (#PCDATA)>
+<!ELEMENT GenbankSynonym  (#PCDATA)>
+<!ELEMENT GenbankAnamorph (#PCDATA)>
+<!ELEMENT PropValueInt (#PCDATA)>
+<!ELEMENT PropValueBool (#PCDATA)>
+<!ELEMENT PropValueString (#PCDATA)>
+
+<!-- Taxon structural entities -->
+<!ELEMENT TaxaSet ( Taxon* )>
+
+<!ELEMENT Taxon (
+                 TaxId,
+                 ScientificName,
+                 OtherNames?, 
+                 ParentTaxId?,
+                 Rank?, 
+                 Division?,
+                 GeneticCode?,
+                 MitoGeneticCode?,
+                 Lineage?,
+                 LineageEx?,
+                 Citations?,
+                 Modifiers?,
+                 Properties?,
+                 CreateDate?,
+                 UpdateDate?,
+                 PubDate?,
+                 AkaTaxIds?
+                )>
+
+
+<!ELEMENT OtherNames	( GenbankCommonName?,
+                          GenbankAcronym?,
+                          BlastName?,
+                          ( EquivalentName |
+                            Synonym        |
+                            Acronym        |
+                            Misspelling    |
+                            Anamorph       |
+                            Includes       |
+                            CommonName     |
+                            Inpart         |
+                            Misnomer       |
+                            Teleomorph     |
+                            GenbankSynonym |
+                            GenbankAnamorph
+                          )*,
+                          Name*
+                        )>
+
+<!ELEMENT Name ( ClassCDE, DispName, UniqueName? )>
+
+<!ELEMENT GeneticCode ( GCId, GCName )>
+
+<!ELEMENT MitoGeneticCode ( MGCId, MGCName )>
+
+<!ELEMENT Citations ( Citation+ )>
+
+<!ELEMENT Citation ( CitId,
+                     CitKey,
+                     CitUrl?,
+                     CitText?,
+                     CitPubmedId?,
+                     CitMedlineId?
+                   )>
+
+<!ELEMENT Modifiers ( Modifier+ )>
+
+<!ELEMENT Modifier ( ModId,
+                     ModType,
+                     ModName,
+                     ModGBhidden,
+                     ( RModId | RTaxId )?
+                   )>
+
+<!ELEMENT Properties ( Property+ )>
+
+<!ELEMENT Property ( PropName, ( PropValueInt |
+                                 PropValueBool |
+                                 PropValueString ) )>
+
+<!ELEMENT AkaTaxIds ( TaxId* )>
+
+<!ELEMENT LineageEx ( Taxon* )>

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod

@@ -0,0 +1,34 @@
+<!-- ...................................................................... -->
+<!-- XHTML Inline Style Module  ........................................... -->
+<!-- file: xhtml-inlstyle-1.mod
+
+     This is XHTML, a reformulation of HTML as a modular XML application.
+     Copyright 1998-2005 W3C (MIT, ERCIM, Keio), All Rights Reserved.
+     Revision: $Id: xhtml-inlstyle-1.mod,v 4.0 2001/04/02 22:42:49 altheim Exp $
+
+     This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+       PUBLIC "-//W3C//ENTITIES XHTML Inline Style 1.0//EN"
+       SYSTEM "http://www.w3.org/MarkUp/DTD/xhtml-inlstyle-1.mod"
+
+     Revisions:
+     (none)
+     ....................................................................... -->
+
+<!-- Inline Style
+
+     This module declares the 'style' attribute, used to support inline
+     style markup. This module must be instantiated prior to the XHTML
+     Common Attributes module in order to be included in %Core.attrib;.
+-->
+
+<!ENTITY % style.attrib
+     "style        CDATA                    #IMPLIED"
+>
+
+
+<!ENTITY % Core.extra.attrib
+     "%style.attrib;"
+>
+
+<!-- end of xhtml-inlstyle-1.mod -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/xhtml-table-1.mod

@@ -0,0 +1,333 @@
+<!-- ...................................................................... -->
+<!-- XHTML Table Module  .................................................. -->
+<!-- file: xhtml-table-1.mod
+
+     This is XHTML, a reformulation of HTML as a modular XML application.
+     Copyright 1998-2005 W3C (MIT, ERCIM, Keio), All Rights Reserved.
+     Revision: $Id: xhtml-table-1.mod,v 4.1 2001/04/10 09:42:30 altheim Exp $ SMI
+
+     This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+       PUBLIC "-//W3C//ELEMENTS XHTML Tables 1.0//EN"
+       SYSTEM "http://www.w3.org/MarkUp/DTD/xhtml-table-1.mod"
+
+     Revisions:
+     (none)
+     ....................................................................... -->
+
+<!-- Tables
+
+        table, caption, thead, tfoot, tbody, colgroup, col, tr, th, td
+
+     This module declares element types and attributes used to provide
+     table markup similar to HTML 4, including features that enable
+     better accessibility for non-visual user agents.
+-->
+
+<!-- declare qualified element type names:
+-->
+<!ENTITY % table.qname  "table" >
+<!ENTITY % caption.qname  "caption" >
+<!ENTITY % thead.qname  "thead" >
+<!ENTITY % tfoot.qname  "tfoot" >
+<!ENTITY % tbody.qname  "tbody" >
+<!ENTITY % colgroup.qname  "colgroup" >
+<!ENTITY % col.qname  "col" >
+<!ENTITY % tr.qname  "tr" >
+<!ENTITY % th.qname  "th" >
+<!ENTITY % td.qname  "td" >
+
+<!-- The frame attribute specifies which parts of the frame around
+     the table should be rendered. The values are not the same as
+     CALS to avoid a name clash with the valign attribute.
+-->
+<!ENTITY % frame.attrib
+     "frame        ( void
+                   | above
+                   | below
+                   | hsides
+                   | lhs
+                   | rhs
+                   | vsides
+                   | box
+                   | border )               #IMPLIED"
+>
+
+<!-- The rules attribute defines which rules to draw between cells:
+
+     If rules is absent then assume:
+
+       "none" if border is absent or border="0" otherwise "all"
+-->
+<!ENTITY % rules.attrib
+     "rules        ( none
+                   | groups
+                   | rows
+                   | cols
+                   | all )                  #IMPLIED"
+>
+
+<!-- horizontal alignment attributes for cell contents
+-->
+<!ENTITY % CellHAlign.attrib
+     "align        ( left
+                   | center
+                   | right
+                   | justify
+                   | char )                 #IMPLIED
+      char         %Character.datatype;     #IMPLIED
+      charoff      %Length.datatype;        #IMPLIED"
+>
+
+<!-- vertical alignment attribute for cell contents
+-->
+<!ENTITY % CellVAlign.attrib
+     "valign       ( top
+                   | middle
+                   | bottom
+                   | baseline )             #IMPLIED"
+>
+
+<!-- scope is simpler than axes attribute for common tables
+-->
+<!ENTITY % scope.attrib
+     "scope        ( row
+                   | col
+                   | rowgroup
+                   | colgroup )             #IMPLIED"
+>
+
+<!-- table: Table Element .............................. -->
+
+<!ENTITY % table.element  "INCLUDE" >
+<![%table.element;[
+<!ENTITY % table.content
+     "( %caption.qname;?, ( %col.qname;* | %colgroup.qname;* ),
+      (( %thead.qname;?, %tfoot.qname;?, %tbody.qname;+ ) | ( %tr.qname;+ )))"
+>
+<!ELEMENT %table.qname;  %table.content; >
+<!-- end of table.element -->]]>
+
+<!ENTITY % table.attlist  "INCLUDE" >
+<![%table.attlist;[
+<!ATTLIST %table.qname;
+      %Common.attrib;
+      summary      %Text.datatype;          #IMPLIED
+      width        %Length.datatype;        #IMPLIED
+      border       %Pixels.datatype;        #IMPLIED
+      %frame.attrib;
+      %rules.attrib;
+      cellspacing  %Length.datatype;        #IMPLIED
+      cellpadding  %Length.datatype;        #IMPLIED
+>
+<!-- end of table.attlist -->]]>
+
+<!-- caption: Table Caption ............................ -->
+
+<!ENTITY % caption.element  "INCLUDE" >
+<![%caption.element;[
+<!ENTITY % caption.content
+     "( #PCDATA | %Inline.mix; )*"
+>
+<!ELEMENT %caption.qname;  %caption.content; >
+<!-- end of caption.element -->]]>
+
+<!ENTITY % caption.attlist  "INCLUDE" >
+<![%caption.attlist;[
+<!ATTLIST %caption.qname;
+      %Common.attrib;
+>
+<!-- end of caption.attlist -->]]>
+
+<!-- thead: Table Header ............................... -->
+
+<!-- Use thead to duplicate headers when breaking table
+     across page boundaries, or for static headers when
+     tbody sections are rendered in scrolling panel.
+-->
+
+<!ENTITY % thead.element  "INCLUDE" >
+<![%thead.element;[
+<!ENTITY % thead.content  "( %tr.qname; )+" >
+<!ELEMENT %thead.qname;  %thead.content; >
+<!-- end of thead.element -->]]>
+
+<!ENTITY % thead.attlist  "INCLUDE" >
+<![%thead.attlist;[
+<!ATTLIST %thead.qname;
+      %Common.attrib;
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of thead.attlist -->]]>
+
+<!-- tfoot: Table Footer ............................... -->
+
+<!-- Use tfoot to duplicate footers when breaking table
+     across page boundaries, or for static footers when
+     tbody sections are rendered in scrolling panel.
+-->
+
+<!ENTITY % tfoot.element  "INCLUDE" >
+<![%tfoot.element;[
+<!ENTITY % tfoot.content  "( %tr.qname; )+" >
+<!ELEMENT %tfoot.qname;  %tfoot.content; >
+<!-- end of tfoot.element -->]]>
+
+<!ENTITY % tfoot.attlist  "INCLUDE" >
+<![%tfoot.attlist;[
+<!ATTLIST %tfoot.qname;
+      %Common.attrib;
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of tfoot.attlist -->]]>
+
+<!-- tbody: Table Body ................................. -->
+
+<!-- Use multiple tbody sections when rules are needed
+     between groups of table rows.
+-->
+
+<!ENTITY % tbody.element  "INCLUDE" >
+<![%tbody.element;[
+<!ENTITY % tbody.content  "( %tr.qname; )+" >
+<!ELEMENT %tbody.qname;  %tbody.content; >
+<!-- end of tbody.element -->]]>
+
+<!ENTITY % tbody.attlist  "INCLUDE" >
+<![%tbody.attlist;[
+<!ATTLIST %tbody.qname;
+      %Common.attrib;
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of tbody.attlist -->]]>
+
+<!-- colgroup: Table Column Group ...................... -->
+
+<!-- colgroup groups a set of col elements. It allows you
+     to group several semantically-related columns together.
+-->
+
+<!ENTITY % colgroup.element  "INCLUDE" >
+<![%colgroup.element;[
+<!ENTITY % colgroup.content  "( %col.qname; )*" >
+<!ELEMENT %colgroup.qname;  %colgroup.content; >
+<!-- end of colgroup.element -->]]>
+
+<!ENTITY % colgroup.attlist  "INCLUDE" >
+<![%colgroup.attlist;[
+<!ATTLIST %colgroup.qname;
+      %Common.attrib;
+      span         %Number.datatype;        '1'
+      width        %MultiLength.datatype;   #IMPLIED
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of colgroup.attlist -->]]>
+
+<!-- col: Table Column ................................. -->
+
+<!-- col elements define the alignment properties for
+     cells in one or more columns.
+
+     The width attribute specifies the width of the
+     columns, e.g.
+
+       width="64"        width in screen pixels
+       width="0.5*"      relative width of 0.5
+
+     The span attribute causes the attributes of one
+     col element to apply to more than one column.
+-->
+
+<!ENTITY % col.element  "INCLUDE" >
+<![%col.element;[
+<!ENTITY % col.content  "EMPTY" >
+<!ELEMENT %col.qname;  %col.content; >
+<!-- end of col.element -->]]>
+
+<!ENTITY % col.attlist  "INCLUDE" >
+<![%col.attlist;[
+<!ATTLIST %col.qname;
+      %Common.attrib;
+      span         %Number.datatype;        '1'
+      width        %MultiLength.datatype;   #IMPLIED
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of col.attlist -->]]>
+
+<!-- tr: Table Row ..................................... -->
+
+<!ENTITY % tr.element  "INCLUDE" >
+<![%tr.element;[
+<!ENTITY % tr.content  "( %th.qname; | %td.qname; )+" >
+<!ELEMENT %tr.qname;  %tr.content; >
+<!-- end of tr.element -->]]>
+
+<!ENTITY % tr.attlist  "INCLUDE" >
+<![%tr.attlist;[
+<!ATTLIST %tr.qname;
+      %Common.attrib;
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of tr.attlist -->]]>
+
+<!-- th: Table Header Cell ............................. -->
+
+<!-- th is for header cells, td for data,
+     but for cells acting as both use td
+-->
+
+<!ENTITY % th.element  "INCLUDE" >
+<![%th.element;[
+<!ENTITY % th.content
+     "( #PCDATA | %Flow.mix; )*"
+>
+<!ELEMENT %th.qname;  %th.content; >
+<!-- end of th.element -->]]>
+
+<!ENTITY % th.attlist  "INCLUDE" >
+<![%th.attlist;[
+<!ATTLIST %th.qname;
+      %Common.attrib;
+      abbr         %Text.datatype;          #IMPLIED
+      axis         CDATA                    #IMPLIED
+      headers      IDREFS                   #IMPLIED
+      %scope.attrib;
+      rowspan      %Number.datatype;        '1'
+      colspan      %Number.datatype;        '1'
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of th.attlist -->]]>
+
+<!-- td: Table Data Cell ............................... -->
+
+<!ENTITY % td.element  "INCLUDE" >
+<![%td.element;[
+<!ENTITY % td.content
+     "( #PCDATA | %Flow.mix; )*"
+>
+<!ELEMENT %td.qname;  %td.content; >
+<!-- end of td.element -->]]>
+
+<!ENTITY % td.attlist  "INCLUDE" >
+<![%td.attlist;[
+<!ATTLIST %td.qname;
+      %Common.attrib;
+      abbr         %Text.datatype;          #IMPLIED
+      axis         CDATA                    #IMPLIED
+      headers      IDREFS                   #IMPLIED
+      %scope.attrib;
+      rowspan      %Number.datatype;        '1'
+      colspan      %Number.datatype;        '1'
+      %CellHAlign.attrib;
+      %CellVAlign.attrib;
+>
+<!-- end of td.attlist -->]]>
+
+<!-- end of xhtml-table-1.mod -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/DTDs/xmlspecchars.ent

@@ -0,0 +1,290 @@
+<!-- ============================================================= -->
+<!--  MODULE:    XML Special Characters Module                     -->
+<!--  VERSION:   2.0                                               -->
+<!--  DATE:      August 2004                                       -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!--                    PUBLIC DOCUMENT TYPE DEFINITION            -->
+<!--                        TYPICAL INVOCATION                     -->
+<!--
+"-//NLM//DTD Archiving and Interchange DTD Suite XML Special Characters Module v2.0 20040830//EN"
+     Delivered as file "xmlspecchars.ent"                          -->
+<!-- ============================================================= -->
+
+<!-- ============================================================= -->
+<!-- SYSTEM:     Archiving and Interchange DTD Suite               -->
+<!--                                                               -->
+<!-- PURPOSE:    External Parameter Entities for calling in the    -->
+<!--             special character entities                        -->
+<!--                                                               -->
+<!-- CONTAINS:   1) Calls to external entity sets                  -->
+<!--                                                               -->
+<!-- MODULES REQUIRED:                                             -->
+<!--             The standard ISO special character entity sets    -->
+<!--             (see below)                                       -->
+<!--                                                               -->
+<!-- CREATED FOR:                                                  -->
+<!--             Digital archives and publishers who wish to       -->
+<!--             create a custom XML DTD for original markup of    -->
+<!--             journal literature, books, and related material,  -->
+<!--             or for archiving and transferring such material   -->
+<!--             between archives.                                 -->
+<!--                                                               -->
+<!--             This DTD is in the public domain. An organization -->
+<!--             that wishes to create its own DTD from the suite  -->
+<!--             may do so without permission from NLM.            -->
+<!--                                                               -->
+<!--             The suite has been set up to be extended using a  -->
+<!--             new DTD file and a new DTD-specific customization -->
+<!--             module to redefine the many Parameter Entities.   -->
+<!--             Do not modify the suite directly or redistribute  -->
+<!--             modified versions of the suite.                   -->
+<!--                                                               -->
+<!--             In the interest of maintaining consistency and    -->
+<!--             clarity for potential users, NLM requests:        -->
+<!--                                                               -->
+<!--             1. If you create a DTD from the Archiving and     -->
+<!--                Interchange DTD Suite and intend to stay       -->
+<!--                compatible with the suite, then please include -->
+<!--                the following statement as a comment in all of -->
+<!--                your DTD modules:                              -->
+<!--                   "Created from, and fully compatible with,   -->
+<!--                    the Archiving and Interchange DTD Suite."  -->
+<!--                                                               -->
+<!--             2. If you alter one or more modules of the suite, -->
+<!--                then please rename your version and all its    -->
+<!--                modules to avoid any confusion with the        -->
+<!--                original suite. Also, please include the       -->
+<!--                following statement as a comment in all your   -->
+<!--                DTD modules:                                   -->
+<!--                   "Based in part on, but not fully compatible -->
+<!--                    with, the Archiving and Interchange DTD    --> 
+<!--                    Suite."                                    -->
+<!--                                                               -->
+<!--             Suggestions for refinements and enhancements to   -->
+<!--             the DTD suite should be sent in email to:         -->
+<!--                 archive-dtd@ncbi.nlm.nih.gov                  -->
+<!--                                                               -->
+<!-- ORIGINAL CREATION DATE:                                       -->
+<!--             December 2002                                     -->
+<!--                                                               -->
+<!-- CREATED BY: Jeff Beck       (NCBI)                            -->
+<!--             Deborah Lapeyre (Mulberry Technologies, Inc.)     -->
+<!--             Bruce Rosenblum (Inera Inc.)                      -->
+<!--                                                               -->
+<!--             NLM thanks the Harvard University Libraries, both -->
+<!--             for proposing that a draft archiving NLM DTD for  --> 
+<!--             life sciences journals be extended to accommodate -->
+<!--             journals in all disciplines and for sponsoring    -->
+<!--             Bruce Rosenblum's collaboration with other DTD    -->
+<!--             authors in completing Version 1.0. The Andrew W.  --> 
+<!--             Mellon Foundation provided support for these      --> 
+<!--             important contributions.                          -->
+<!--                                                               -->
+<!-- ============================================================= -->
+
+
+<!-- ============================================================= -->
+<!--                    DTD VERSION/CHANGE HISTORY                 -->
+<!-- ============================================================= -->
+<!--
+     =============================================================
+
+Version  Reason/Occasion                   (who) vx.x (yyyy-mm-dd)
+     
+     Major requirement changes led to the new release, producing
+     DTD version "2.0":
+       a) The splitting of the Archival and Interchange Tag Set 
+          DTDs into three DTDs from two: an authoring DTD, an
+          archive regularization and interchange DTD (the
+          current Blue Publishing DTD), and a preservationist 
+          archive DTD (the current Green Archiving and Interchange 
+          DTD).
+       b) AIT Working Group suggestions from the June 04 meeting 
+          and June/July 2004 followup discussions
+       c) Suite remodularization to meet new (and newly articulated)
+          modularization requirements
+       d) New or renamed classes and mixes to make modifications
+          easier and more consistent
+
+  1. Updated public identifier to "v2.0 20040830"          
+                                                                   -->
+
+
+<!-- ============================================================= -->
+<!--                    ISO STANDARD SPECIAL CHARACTER SETS DEFINED-->
+<!-- ============================================================= -->
+
+
+<!--                    ISO STANDARD ADDED LATIN 1                 -->
+<!ENTITY % ISOlat1 PUBLIC
+"-//W3C//ENTITIES Added Latin 1 for MathML 2.0//EN" 
+"xmlchars/isolat1.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED LATIN 2                 -->
+<!ENTITY % ISOlat2 PUBLIC
+"-//W3C//ENTITIES Added Latin 2 for MathML 2.0//EN" 
+"xmlchars/isolat2.ent"                                               >
+
+
+<!--                    ISO BOX AND LINE DRAWING                   -->
+<!ENTITY % ISObox       PUBLIC 
+"-//W3C//ENTITIES Box and Line Drawing for MathML 2.0//EN"
+"xmlchars/isobox.ent"                                               >
+
+
+<!--                    ISO STANDARD DIACRITICAL MARKS             -->
+<!ENTITY % ISOdia PUBLIC
+"-//W3C//ENTITIES Diacritical Marks for MathML 2.0//EN" 
+"xmlchars/isodia.ent"                                                >
+
+
+<!--                    ISO STANDARD NUMERIC AND SPECIAL GRAPHIC   -->
+<!ENTITY % ISOnum PUBLIC
+"-//W3C//ENTITIES Numeric and Special Graphic for MathML 2.0//EN" 
+"xmlchars/isonum.ent"                                                >
+
+
+<!--                    ISO STANDARD PUBLISHING                    -->
+<!ENTITY % ISOpub PUBLIC
+"-//W3C//ENTITIES Publishing for MathML 2.0//EN" 
+"xmlchars/isopub.ent"                                                >
+
+
+<!--                    ISO STANDARD GENERAL TECHNICAL             -->
+<!ENTITY % ISOtech PUBLIC
+"-//W3C//ENTITIES General Technical for MathML 2.0//EN" 
+"xmlchars/isotech.ent"                                               >
+
+
+<!--                    ISO STANDARD GREEK LETTERS                 -->
+<!ENTITY % ISOgrk1 PUBLIC
+"-//W3C//ENTITIES Greek Letters//EN"
+"xmlchars/isogrk1.ent"                                               >
+
+
+<!--                    ISO STANDARD MONOTONIKO GREEK              -->
+<!ENTITY % ISOgrk2 PUBLIC
+"-//W3C//ENTITIES Monotoniko Greek//EN"
+"xmlchars/isogrk2.ent"                                               >
+
+
+<!--                    ISO STANDARD GREEK SYMBOLS                 -->
+<!ENTITY % ISOgrk3 PUBLIC
+"-//W3C//ENTITIES Greek Symbols for MathML 2.0//EN"
+"xmlchars/isogrk3.ent"                                               >
+
+
+<!--                    ISO STANDARD ALTERNATIVE GREEK SYMBOLS     -->
+<!ENTITY % ISOgrk4 PUBLIC
+"-//W3C//ENTITIES Alternative Greek Symbols//EN"
+"xmlchars/isogrk4.ent"                                               >
+
+
+<!--                    ISO STANDARD RUSSIAN CYRILLIC              -->
+<!ENTITY % ISOcyr1 PUBLIC 
+"-//W3C//ENTITIES Russian Cyrillic for MathML 2.0//EN" 
+"xmlchars/isocyr1.ent"                                               >
+
+
+<!--                    ISO STANDARD NON-RUSSIAN CYRILLIC          -->
+<!ENTITY % ISOcyr2 PUBLIC
+"-//W3C//ENTITIES Non-Russian Cyrillic for MathML 2.0//EN" 
+"xmlchars/isocyr2.ent"                                               >
+
+
+<!--                    ISO STANDARD MATH ALPHABETS (SCRIPT)       -->
+<!ENTITY % ISOmscr PUBLIC
+"-//W3C//ENTITIES Math Alphabets: Script for MathML 2.0//EN" 
+"xmlchars/isomscr.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS 
+                           (ARROW RELATIONS)                       -->
+<!ENTITY % ISOamsa PUBLIC
+"-//W3C//ENTITIES Added Math Symbols: Arrow Relations for MathML 2.0//EN" 
+"xmlchars/isoamsa.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS 
+                           (BINARY OPERATORS)                      -->
+<!ENTITY % ISOamsb PUBLIC 
+"-//W3C//ENTITIES Added Math Symbols: Binary Operators for MathML 2.0//EN" 
+"xmlchars/isoamsb.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS 
+                           (DELIMITERS)                            -->
+<!ENTITY % ISOamsc PUBLIC 
+"-//W3C//ENTITIES Added Math Symbols: Delimiters for MathML 2.0//EN" 
+"xmlchars/isoamsc.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS 
+                           (NEGATED RELATIONS)                     -->
+<!ENTITY % ISOamsn PUBLIC 
+"-//W3C//ENTITIES Added Math Symbols: Negated Relations for MathML 2.0//EN"
+"xmlchars/isoamsn.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS (ORDINARY) -->
+<!ENTITY % ISOamso PUBLIC 
+"-//W3C//ENTITIES Added Math Symbols: Ordinary for MathML 2.0//EN" 
+"xmlchars/isoamso.ent"                                               >
+
+
+<!--                    ISO STANDARD ADDED MATH SYMBOLS 
+                           (RELATIONS)                             -->
+<!ENTITY % ISOamsr PUBLIC 
+"-//W3C//ENTITIES Added Math Symbols: Relations for MathML 2.0//EN" 
+"xmlchars/isoamsr.ent"                                               >
+
+
+<!--                    ISO STANDARD MATH ALPHABETS (FRAKTUR)      -->
+<!ENTITY % ISOmfrk PUBLIC
+"-//W3C//ENTITIES Math Alphabets: Fraktur for MathML 2.0//EN" 
+"xmlchars/isomfrk.ent"                                               >
+
+
+<!--                    ISO STANDARD MATH ALPHABETS (OPEN FACE)    -->
+<!ENTITY % ISOmopf PUBLIC
+"-//W3C//ENTITIES Math Alphabets: Open Face for MathML 2.0//EN" 
+"xmlchars/isomopf.ent"                                               >
+
+
+<!-- ============================================================= -->
+<!--                    ISO SPECIAL CHARACTER SETS INVOKED         -->
+<!-- ============================================================= -->
+
+
+%ISOlat1;
+%ISOlat2;
+%ISObox;
+%ISOdia;
+%ISOnum;
+%ISOpub;
+%ISOtech;
+%ISOgrk1;
+%ISOgrk2;
+%ISOgrk3;
+%ISOgrk4;
+%ISOcyr1;
+%ISOcyr2;
+%ISOamsa;
+%ISOamsb;
+%ISOamsc;
+%ISOamsn;
+%ISOamso;
+%ISOamsr;
+%ISOmscr;
+%ISOmfrk; 
+%ISOmopf;
+
+
+<!--                    Custom special characters are declared 
+                        in a separate module %chars.ent;           -->
+
+
+<!-- ============ End of XML Special Characters Module =========== -->

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/Parser.py

@@ -0,0 +1,1165 @@
+# Copyright 2008-2014 by Michiel de Hoon.  All rights reserved.
+# Revisions copyright 2008-2015 by Peter Cock. All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+
+"""Parser for XML results returned by NCBI's Entrez Utilities.
+
+This parser is used by the read() function in Bio.Entrez, and is not
+intended be used directly.
+
+The question is how to represent an XML file as Python objects. Some
+XML files returned by NCBI look like lists, others look like dictionaries,
+and others look like a mix of lists and dictionaries.
+
+My approach is to classify each possible element in the XML as a plain
+string, an integer, a list, a dictionary, or a structure. The latter is a
+dictionary where the same key can occur multiple times; in Python, it is
+represented as a dictionary where that key occurs once, pointing to a list
+of values found in the XML file.
+
+The parser then goes through the XML and creates the appropriate Python
+object for each element. The different levels encountered in the XML are
+preserved on the Python side. So a subelement of a subelement of an element
+is a value in a dictionary that is stored in a list which is a value in
+some other dictionary (or a value in a list which itself belongs to a list
+which is a value in a dictionary, and so on). Attributes encountered in
+the XML are stored as a dictionary in a member .attributes of each element,
+and the tag name is saved in a member .tag.
+
+To decide which kind of Python object corresponds to each element in the
+XML, the parser analyzes the DTD referred at the top of (almost) every
+XML file returned by the Entrez Utilities. This is preferred over a hand-
+written solution, since the number of DTDs is rather large and their
+contents may change over time. About half the code in this parser deals
+with parsing the DTD, and the other half with the XML itself.
+"""
+
+import os
+import warnings
+import xml.etree.ElementTree as ET
+from collections import Counter
+from io import BytesIO
+from urllib.parse import urlparse
+from urllib.request import urlopen
+from xml.parsers import expat
+from xml.sax.saxutils import escape
+
+from Bio import StreamModeError
+
+# The following four classes are used to add a member .attributes to integers,
+# strings, lists, and dictionaries, respectively.
+
+
+class NoneElement:
+    """NCBI Entrez XML element mapped to None."""
+
+    def __init__(self, tag, attributes, key):
+        """Create a NoneElement."""
+        self.tag = tag
+        self.key = key
+        self.attributes = attributes
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        try:
+            attributes = self.attributes
+        except AttributeError:
+            return "NoneElement"
+        return "NoneElement(attributes=%r)" % attributes
+
+    def __eq__(self, other):
+        if isinstance(other, NoneElement):
+            return True
+        return False
+
+
+class IntegerElement(int):
+    """NCBI Entrez XML element mapped to an integer."""
+
+    def __new__(cls, value, *args, **kwargs):
+        """Create an IntegerElement."""
+        return int.__new__(cls, value)
+
+    def __init__(self, value, tag, attributes, key):
+        """Initialize an IntegerElement."""
+        self.tag = tag
+        self.attributes = attributes
+        self.key = key
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        text = int.__repr__(self)
+        try:
+            attributes = self.attributes
+        except AttributeError:
+            return text
+        return f"IntegerElement({text}, attributes={attributes!r})"
+
+
+class StringElement(str):
+    """NCBI Entrez XML element mapped to a string."""
+
+    def __new__(cls, value, *args, **kwargs):
+        """Create a StringElement."""
+        return str.__new__(cls, value)
+
+    def __init__(self, value, tag, attributes, key):
+        """Initialize a StringElement."""
+        self.tag = tag
+        self.attributes = attributes
+        self.key = key
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        text = str.__repr__(self)
+        attributes = self.attributes
+        if not attributes:
+            return text
+        return f"StringElement({text}, attributes={attributes!r})"
+
+
+class ListElement(list):
+    """NCBI Entrez XML element mapped to a list."""
+
+    def __init__(self, tag, attributes, allowed_tags, key=None):
+        """Create a ListElement."""
+        self.tag = tag
+        if key is None:
+            self.key = tag
+        else:
+            self.key = key
+        self.attributes = attributes
+        self.allowed_tags = allowed_tags
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        text = list.__repr__(self)
+        attributes = self.attributes
+        if not attributes:
+            return text
+        return f"ListElement({text}, attributes={attributes!r})"
+
+    def store(self, value):
+        """Append an element to the list, checking tags."""
+        key = value.key
+        if self.allowed_tags is not None and key not in self.allowed_tags:
+            raise ValueError("Unexpected item '%s' in list" % key)
+        del value.key
+        self.append(value)
+
+
+class DictionaryElement(dict):
+    """NCBI Entrez XML element mapped to a dictionaray."""
+
+    def __init__(self, tag, attrs, allowed_tags, repeated_tags=None, key=None):
+        """Create a DictionaryElement."""
+        self.tag = tag
+        if key is None:
+            self.key = tag
+        else:
+            self.key = key
+        self.attributes = attrs
+        self.allowed_tags = allowed_tags
+        self.repeated_tags = repeated_tags
+        if repeated_tags:
+            for key in repeated_tags:
+                self[key] = []
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        text = dict.__repr__(self)
+        attributes = self.attributes
+        if not attributes:
+            return text
+        return f"DictElement({text}, attributes={attributes!r})"
+
+    def store(self, value):
+        """Add an entry to the dictionary, checking tags."""
+        key = value.key
+        tag = value.tag
+        if self.allowed_tags is not None and tag not in self.allowed_tags:
+            raise ValueError("Unexpected item '%s' in dictionary" % key)
+        del value.key
+        if self.repeated_tags and key in self.repeated_tags:
+            self[key].append(value)
+        else:
+            self[key] = value
+
+
+class OrderedListElement(list):
+    """NCBI Entrez XML element mapped to a list of lists.
+
+    OrderedListElement is used to describe a list of repeating elements such as
+    A, B, C, A, B, C, A, B, C ... where each set of A, B, C forms a group. This
+    is then stored as [[A, B, C], [A, B, C], [A, B, C], ...]
+    """
+
+    def __init__(self, tag, attributes, allowed_tags, first_tag, key=None):
+        """Create an OrderedListElement."""
+        self.tag = tag
+        if key is None:
+            self.key = tag
+        else:
+            self.key = key
+        self.attributes = attributes
+        self.allowed_tags = allowed_tags
+        self.first_tag = first_tag
+
+    def __repr__(self):
+        """Return a string representation of the object."""
+        text = list.__repr__(self)
+        attributes = self.attributes
+        if not attributes:
+            return text
+        return f"OrderedListElement({text}, attributes={attributes!r})"
+
+    def store(self, value):
+        """Append an element to the list, checking tags."""
+        key = value.key
+        if self.allowed_tags is not None and key not in self.allowed_tags:
+            raise ValueError("Unexpected item '%s' in list" % key)
+        if key == self.first_tag:
+            self.append([])
+        self[-1].append(value)
+
+
+class ErrorElement(str):
+    """NCBI Entrez XML element containing an error message."""
+
+    def __new__(cls, value, *args, **kwargs):
+        """Create an ErrorElement."""
+        return str.__new__(cls, value)
+
+    def __init__(self, value, tag):
+        """Initialize an ErrorElement."""
+        self.tag = tag
+        self.key = tag
+
+    def __repr__(self):
+        """Return the error message as a string."""
+        text = str.__repr__(self)
+        return f"ErrorElement({text})"
+
+
+class NotXMLError(ValueError):
+    """Failed to parse file as XML."""
+
+    def __init__(self, message):
+        """Initialize the class."""
+        self.msg = message
+
+    def __str__(self):
+        """Return a string summary of the exception."""
+        return (
+            "Failed to parse the XML data (%s). Please make sure that the input data "
+            "are in XML format." % self.msg
+        )
+
+
+class CorruptedXMLError(ValueError):
+    """Corrupted XML."""
+
+    def __init__(self, message):
+        """Initialize the class."""
+        self.msg = message
+
+    def __str__(self):
+        """Return a string summary of the exception."""
+        return (
+            "Failed to parse the XML data (%s). Please make sure that the input data "
+            "are not corrupted." % self.msg
+        )
+
+
+class ValidationError(ValueError):
+    """XML tag found which was not defined in the DTD.
+
+    Validating parsers raise this error if the parser finds a tag in the XML
+    that is not defined in the DTD. Non-validating parsers do not raise this
+    error. The Bio.Entrez.read and Bio.Entrez.parse functions use validating
+    parsers by default (see those functions for more information).
+    """
+
+    def __init__(self, name):
+        """Initialize the class."""
+        self.name = name
+
+    def __str__(self):
+        """Return a string summary of the exception."""
+        return (
+            "Failed to find tag '%s' in the DTD. To skip all tags that "
+            "are not represented in the DTD, please call Bio.Entrez.read "
+            "or Bio.Entrez.parse with validate=False." % self.name
+        )
+
+
+class DataHandlerMeta(type):
+    """A metaclass is needed until Python supports @classproperty."""
+
+    def __init__(cls, *args, **kwargs):
+        """Initialize the class."""
+        from Bio import Entrez
+
+        try:
+            cls.directory = Entrez.local_cache  # use default directory for local cache
+        except PermissionError:
+            cls._directory = Entrez.local_cache  # no local cache
+        del Entrez
+
+    @property
+    def directory(cls):
+        """Directory for caching XSD and DTD files."""
+        return cls._directory
+
+    @directory.setter
+    def directory(cls, value):
+        """Set a custom directory for the local DTD/XSD directories."""
+        if value is None:
+            import platform
+
+            if platform.system() == "Windows":
+                value = os.path.join(os.getenv("APPDATA"), "biopython")
+            else:  # Unix/Linux/Mac
+                home = os.path.expanduser("~")
+                value = os.path.join(home, ".config", "biopython")
+        # Create DTD local directory
+        cls.local_dtd_dir = os.path.join(value, "Bio", "Entrez", "DTDs")
+        os.makedirs(cls.local_dtd_dir, exist_ok=True)
+        # Create XSD local directory
+        cls.local_xsd_dir = os.path.join(value, "Bio", "Entrez", "XSDs")
+        os.makedirs(cls.local_xsd_dir, exist_ok=True)
+        # Save the directory name after creating the DTD and XSD local
+        # directories to ensure there was no PermissionError.
+        cls._directory = value
+
+
+class DataHandler(metaclass=DataHandlerMeta):
+    """Data handler for parsing NCBI XML from Entrez."""
+
+    from Bio import Entrez
+
+    global_dtd_dir = os.path.join(Entrez.__path__[0], "DTDs")
+    global_xsd_dir = os.path.join(Entrez.__path__[0], "XSDs")
+    local_dtd_dir = None
+    local_xsd_dir = None
+
+    del Entrez
+
+    def __init__(self, validate, escape, ignore_errors):
+        """Create a DataHandler object."""
+        self.dtd_urls = []
+        self.element = None
+        self.level = 0
+        self.bypass_url_security = False
+        self.data = []
+        self.attributes = None
+        self.allowed_tags = None
+        self.constructors = {}
+        self.strings = {}
+        self.items = set()
+        self.errors = set()
+        self.validating = validate
+        self.ignore_errors = ignore_errors
+        self.parser = expat.ParserCreate(namespace_separator=" ")
+        self.parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)
+        self.parser.XmlDeclHandler = self.xmlDeclHandler
+        self.schema_namespace = None
+        self.namespace_level = Counter()
+        self.namespace_prefix = {}
+        if escape:
+            self.characterDataHandler = self.characterDataHandlerEscape
+        else:
+            self.characterDataHandler = self.characterDataHandlerRaw
+
+    def read(self, source):
+        """Set up the parser and let it read the XML results."""
+        # Expat's parser.ParseFile function only accepts binary data;
+        # see also the comment below for Entrez.parse.
+        try:
+            stream = open(source, "rb")
+        except TypeError:  # not a path, assume we received a stream
+            if source.read(0) != b"":
+                raise StreamModeError(
+                    "the XML file must be opened in binary mode."
+                ) from None
+            stream = source
+        if stream.read(0) != b"":
+            raise TypeError("file should be opened in binary mode")
+        try:
+            self.parser.ParseFile(stream)
+        except expat.ExpatError as e:
+            if self.parser.StartElementHandler:
+                # We saw the initial <!xml declaration, so we can be sure that
+                # we are parsing XML data. Most likely, the XML file is
+                # corrupted.
+                raise CorruptedXMLError(e) from None
+            else:
+                # We have not seen the initial <!xml declaration, so probably
+                # the input data is not in XML format.
+                raise NotXMLError(e) from None
+        finally:
+            if stream is not source:
+                stream.close()
+        try:
+            record = self.record
+        except AttributeError:
+            if self.parser.StartElementHandler:
+                # We saw the initial <!xml declaration, and expat didn't notice
+                # any errors, so self.record should be defined. If not, this is
+                # a bug.
+                raise RuntimeError(
+                    "Failed to parse the XML file correctly, possibly due to a bug "
+                    "in Bio.Entrez. Please contact the Biopython developers via "
+                    "the mailing list or GitHub for assistance."
+                ) from None
+            else:
+                # We did not see the initial <!xml declaration, so probably
+                # the input data is not in XML format.
+                raise NotXMLError("XML declaration not found") from None
+        else:
+            del record.key
+            return record
+
+    def parse(self, source):
+        """Set up the parser and let it read the XML results."""
+        # The source must be a filename, or a file-like object opened in binary
+        # mode. Data read from the file or file-like object as bytes. Expat will
+        # pick up the encoding from the XML declaration (or assume UTF-8 if it
+        # is missing), and use this encoding to convert the binary data to a
+        # string before giving it to characterDataHandler.
+        # While parser.ParseFile only accepts binary data, parser.Parse accepts
+        # both binary data and strings. However, a file in text mode may have
+        # been opened with an encoding different from the encoding specified in
+        # the XML declaration at the top of the file. If so, the data in the
+        # file will have been decoded with an incorrect encoding. To avoid
+        # this, and to be consistent with parser.ParseFile (which is used in
+        # the Entrez.read function above), we require the source data to be in
+        # binary mode here as well.
+        try:
+            stream = open(source, "rb")
+        except TypeError:  # not a path, assume we received a stream
+            if source.read(0) != b"":
+                raise StreamModeError(
+                    "the XML file must be opened in binary mode."
+                ) from None
+            stream = source
+        if stream.read(0) != b"":
+            raise TypeError("file should be opened in binary mode")
+        BLOCK = 1024
+        try:
+            while True:
+                # Read in another block of data from the file.
+                data = stream.read(BLOCK)
+                self.parser.Parse(data, False)
+                try:
+                    records = self.record
+                except AttributeError:
+                    if self.parser.StartElementHandler:
+                        # We saw the initial <!xml declaration, and expat
+                        # didn't notice any errors, so self.record should be
+                        # defined. If not, this is a bug.
+
+                        raise RuntimeError(
+                            "Failed to parse the XML file correctly, possibly due to a "
+                            "bug in Bio.Entrez. Please contact the Biopython "
+                            "developers via the mailing list or GitHub for assistance."
+                        ) from None
+                    else:
+                        # We did not see the initial <!xml declaration, so
+                        # probably the input data is not in XML format.
+                        raise NotXMLError("XML declaration not found") from None
+
+                if not isinstance(records, list):
+                    raise ValueError(
+                        "The XML file does not represent a list. Please use "
+                        "Entrez.read instead of Entrez.parse."
+                    )
+
+                if not data:
+                    break
+
+                while len(records) >= 2:
+                    # Then the first record is finished, while the second record
+                    # is still a work in progress.
+                    record = records.pop(0)
+                    yield record
+
+        except expat.ExpatError as e:
+            if self.parser.StartElementHandler:
+                # We saw the initial <!xml declaration, so we can be sure
+                # that we are parsing XML data. Most likely, the XML file
+                # is corrupted.
+                raise CorruptedXMLError(e) from None
+            else:
+                # We have not seen the initial <!xml declaration, so
+                # probably the input data is not in XML format.
+                raise NotXMLError(e) from None
+        finally:
+            if stream is not source:
+                stream.close()
+
+        # We have reached the end of the XML file
+        self.parser = None
+        if self.element is not None:
+            # No more XML data, but there is still some unfinished business
+            raise CorruptedXMLError("Premature end of data")
+
+        # Send out the remaining records
+        yield from records
+
+    def xmlDeclHandler(self, version, encoding, standalone):
+        """Set XML handlers when an XML declaration is found."""
+        self.parser.CharacterDataHandler = self.characterDataHandler
+        self.parser.ExternalEntityRefHandler = self.externalEntityRefHandler
+        self.parser.StartNamespaceDeclHandler = self.startNamespaceDeclHandler
+        self.parser.EndNamespaceDeclHandler = self.endNamespaceDeclHandler
+        self.parser.StartElementHandler = self.handleMissingDocumentDefinition
+
+    def handleMissingDocumentDefinition(self, tag, attrs):
+        """Raise an Exception if neither a DTD nor an XML Schema is found."""
+        raise ValueError(
+            "As the XML data contained neither a Document Type Definition (DTD) nor an XML Schema, Bio.Entrez is unable to parse these data. We recommend using a generic XML parser from the Python standard library instead, for example ElementTree."
+        )
+
+    def startNamespaceDeclHandler(self, prefix, uri):
+        """Handle start of an XML namespace declaration."""
+        if prefix == "xsi":
+            # This is an xml schema
+            self.schema_namespace = uri
+            self.parser.StartElementHandler = self.schemaHandler
+        else:
+            # Note that the DTD for MathML specifies a default attribute
+            # that declares the namespace for each MathML element. This means
+            # that MathML element in the XML has an invisible MathML namespace
+            # declaration that triggers a call to startNamespaceDeclHandler
+            # and endNamespaceDeclHandler. Therefore we need to count how often
+            # startNamespaceDeclHandler and endNamespaceDeclHandler were called
+            # to find out their first and last invocation for each namespace.
+            if prefix == "mml":
+                assert uri == "http://www.w3.org/1998/Math/MathML"
+            elif prefix == "xlink":
+                assert uri == "http://www.w3.org/1999/xlink"
+            elif prefix == "ali":
+                assert uri.rstrip("/") == "http://www.niso.org/schemas/ali/1.0"
+            else:
+                raise ValueError(f"Unknown prefix '{prefix}' with uri '{uri}'")
+            self.namespace_level[prefix] += 1
+            self.namespace_prefix[uri] = prefix
+
+    def endNamespaceDeclHandler(self, prefix):
+        """Handle end of an XML namespace declaration."""
+        if prefix != "xsi":
+            self.namespace_level[prefix] -= 1
+            if self.namespace_level[prefix] == 0:
+                for key, value in self.namespace_prefix.items():
+                    if value == prefix:
+                        break
+                else:
+                    raise RuntimeError("Failed to find namespace prefix")
+                del self.namespace_prefix[key]
+
+    def schemaHandler(self, name, attrs):
+        """Process the XML schema (before processing the element)."""
+        key = "%s noNamespaceSchemaLocation" % self.schema_namespace
+        schema = attrs[key]
+        self.verify_security(schema)
+        handle = self.open_xsd_file(os.path.basename(schema))
+        # if there is no local xsd file grab the url and parse the file
+        if not handle:
+            handle = urlopen(schema)
+            text = handle.read()
+            self.save_xsd_file(os.path.basename(schema), text)
+            handle.close()
+            self.parse_xsd(ET.fromstring(text))
+        else:
+            self.parse_xsd(ET.fromstring(handle.read()))
+            handle.close()
+        # continue handling the element
+        self.startElementHandler(name, attrs)
+        # reset the element handler
+        self.parser.StartElementHandler = self.startElementHandler
+
+    def startElementHandler(self, tag, attrs):
+        """Handle start of an XML element."""
+        prefix = None
+        if self.namespace_prefix:
+            try:
+                uri, name = tag.split()
+            except ValueError:
+                pass
+            else:
+                prefix = self.namespace_prefix[uri]
+                tag = f"{prefix}:{name}"
+        if tag in self.items:
+            assert tag == "Item"
+            name = attrs["Name"]
+            itemtype = attrs["Type"]
+            del attrs["Type"]
+            if itemtype == "Structure":
+                del attrs["Name"]
+                element = DictionaryElement(
+                    name, attrs, allowed_tags=None, repeated_tags=None
+                )
+                parent = self.element
+                element.parent = parent
+                # For consistency with lists below, store the element here
+                if parent is None:
+                    self.record = element
+                else:
+                    parent.store(element)
+                self.element = element
+                self.parser.EndElementHandler = self.endElementHandler
+                self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+            elif name in ("ArticleIds", "History"):
+                del attrs["Name"]
+                allowed_tags = None  # allowed tags are unknown
+                repeated_tags = frozenset(["pubmed", "medline"])
+                element = DictionaryElement(
+                    tag,
+                    attrs,
+                    allowed_tags=allowed_tags,
+                    repeated_tags=repeated_tags,
+                    key=name,
+                )
+                parent = self.element
+                element.parent = parent
+                # For consistency with lists below, store the element here
+                if parent is None:
+                    self.record = element
+                else:
+                    parent.store(element)
+                self.element = element
+                self.parser.EndElementHandler = self.endElementHandler
+                self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+            elif itemtype == "List":
+                del attrs["Name"]
+                allowed_tags = None  # allowed tags are unknown
+                element = ListElement(tag, attrs, allowed_tags, name)
+                parent = self.element
+                element.parent = parent
+                if self.element is None:
+                    # Set self.record here to let Entrez.parse iterate over it
+                    self.record = element
+                else:
+                    parent.store(element)
+                self.element = element
+                self.parser.EndElementHandler = self.endElementHandler
+                self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+            elif itemtype == "Integer":
+                self.parser.EndElementHandler = self.endIntegerElementHandler
+                self.parser.CharacterDataHandler = self.characterDataHandler
+                self.attributes = attrs
+            elif itemtype in ("String", "Unknown", "Date", "Enumerator"):
+                assert self.attributes is None
+                self.attributes = attrs
+                self.parser.StartElementHandler = self.startRawElementHandler
+                self.parser.EndElementHandler = self.endStringElementHandler
+                self.parser.CharacterDataHandler = self.characterDataHandler
+            else:
+                raise ValueError("Unknown item type %s" % name)
+        elif tag in self.errors:
+            self.parser.EndElementHandler = self.endErrorElementHandler
+            self.parser.CharacterDataHandler = self.characterDataHandler
+        elif tag in self.strings:
+            self.parser.StartElementHandler = self.startRawElementHandler
+            self.parser.EndElementHandler = self.endStringElementHandler
+            self.parser.CharacterDataHandler = self.characterDataHandler
+            assert self.allowed_tags is None
+            self.allowed_tags = self.strings[tag]
+            assert self.attributes is None
+            self.attributes = attrs
+        elif tag in self.constructors:
+            cls, allowed_tags = self.constructors[tag]
+            element = cls(tag, attrs, *allowed_tags)
+            parent = self.element
+            element.parent = parent
+            if parent is None:
+                # Set self.record here to let Entrez.parse iterate over it
+                self.record = element
+            else:
+                parent.store(element)
+            self.element = element
+            self.parser.EndElementHandler = self.endElementHandler
+            self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+        else:
+            # Element not found in DTD
+            if tag == "processing-meta":
+                terms = []
+                dtd_version = "1.3"
+                if attrs["tagset-family"] == "jats":
+                    terms.append("JATS")
+                if attrs["base-tagset"] == "archiving":
+                    term = "archivearticle" + dtd_version.replace(".", "-")
+                    terms.append(term)
+                if attrs.get("mathml-version") == "3.0":
+                    terms.append("mathml3")
+                basename = "-".join(terms)
+                url = f"https://{attrs['tagset-family']}.nlm.nih.gov/{attrs['base-tagset']}/{dtd_version}/{basename}.dtd"
+                self.xmlDeclHandler(None, None, None)
+                self.externalEntityRefHandler(None, None, url, None)
+                # remainder will be ignored and will not be stored in the record
+            elif self.validating:
+                raise ValidationError(tag)
+            # this will not be stored in the record
+            self.parser.StartElementHandler = self.startSkipElementHandler
+            self.parser.EndElementHandler = self.endSkipElementHandler
+            self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+            self.level = 1
+
+    def startRawElementHandler(self, name, attrs):
+        """Handle start of an XML raw element."""
+        # check if the name is in a namespace
+        prefix = None
+        if self.namespace_prefix:
+            try:
+                uri, name = name.split()
+            except ValueError:
+                pass
+            else:
+                prefix = self.namespace_prefix[uri]
+                if self.namespace_level[prefix] == 1:
+                    attrs = {"xmlns": uri}
+        if prefix:
+            key = f"{prefix}:{name}"
+        else:
+            key = name
+        # self.allowed_tags is ignored for now. Anyway we know what to do
+        # with this tag.
+        tag = "<%s" % name
+        for key, value in attrs.items():
+            tag += f' {key}="{value}"'
+        tag += ">"
+        self.data.append(tag)
+        self.parser.EndElementHandler = self.endRawElementHandler
+        self.level += 1
+
+    def startSkipElementHandler(self, name, attrs):
+        """Handle start of an XML skip element."""
+        self.level += 1
+
+    def endStringElementHandler(self, tag):
+        """Handle end of an XML string element."""
+        element = self.element
+        if element is not None:
+            self.parser.StartElementHandler = self.startElementHandler
+            self.parser.EndElementHandler = self.endElementHandler
+            self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+        data = "".join(self.data)
+        self.data = []
+        attributes = self.attributes
+        self.attributes = None
+        if self.namespace_prefix:
+            try:
+                uri, name = tag.split()
+            except ValueError:
+                pass
+            else:
+                prefix = self.namespace_prefix[uri]
+                tag = f"{prefix}:{name}"
+        if tag in self.items:
+            assert tag == "Item"
+            key = attributes["Name"]
+            del attributes["Name"]
+        else:
+            key = tag
+        value = StringElement(data, tag, attributes, key)
+        if element is None:
+            self.record = element
+        else:
+            element.store(value)
+        self.allowed_tags = None
+
+    def endRawElementHandler(self, name):
+        """Handle end of an XML raw element."""
+        self.level -= 1
+        if self.level == 0:
+            self.parser.EndElementHandler = self.endStringElementHandler
+        if self.namespace_prefix:
+            try:
+                uri, name = name.split()
+            except ValueError:
+                pass
+        tag = "</%s>" % name
+        self.data.append(tag)
+
+    def endSkipElementHandler(self, name):
+        """Handle end of an XML skip element."""
+        self.level -= 1
+        if self.level == 0:
+            self.parser.StartElementHandler = self.startElementHandler
+            self.parser.EndElementHandler = self.endElementHandler
+
+    def endErrorElementHandler(self, tag):
+        """Handle end of an XML error element."""
+        element = self.element
+        if element is not None:
+            self.parser.StartElementHandler = self.startElementHandler
+            self.parser.EndElementHandler = self.endElementHandler
+            self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+        data = "".join(self.data)
+        if data == "":
+            return
+        if self.ignore_errors is False:
+            raise RuntimeError(data)
+        self.data = []
+        value = ErrorElement(data, tag)
+        if element is None:
+            self.record = element
+        else:
+            element.store(value)
+
+    def endElementHandler(self, name):
+        """Handle end of an XML element."""
+        element = self.element
+        self.element = element.parent
+        del element.parent
+
+    def endIntegerElementHandler(self, tag):
+        """Handle end of an XML integer element."""
+        attributes = self.attributes
+        self.attributes = None
+        assert tag == "Item"
+        key = attributes["Name"]
+        del attributes["Name"]
+        if self.data:
+            value = int("".join(self.data))
+            self.data = []
+            value = IntegerElement(value, tag, attributes, key)
+        else:
+            value = NoneElement(tag, attributes, key)
+        element = self.element
+        if element is None:
+            self.record = value
+        else:
+            self.parser.EndElementHandler = self.endElementHandler
+            self.parser.CharacterDataHandler = self.skipCharacterDataHandler
+            if value is None:
+                return
+            element.store(value)
+
+    def characterDataHandlerRaw(self, content):
+        """Handle character data as-is (raw)."""
+        self.data.append(content)
+
+    def characterDataHandlerEscape(self, content):
+        """Handle character data by encoding it."""
+        content = escape(content)
+        self.data.append(content)
+
+    def skipCharacterDataHandler(self, content):
+        """Handle character data by skipping it."""
+
+    def parse_xsd(self, root):
+        """Parse an XSD file."""
+        prefix = "{http://www.w3.org/2001/XMLSchema}"
+        for element in root:
+            isSimpleContent = False
+            attribute_keys = []
+            keys = []
+            multiple = []
+            assert element.tag == prefix + "element"
+            name = element.attrib["name"]
+            assert len(element) == 1
+            complexType = element[0]
+            assert complexType.tag == prefix + "complexType"
+            for component in complexType:
+                tag = component.tag
+                if tag == prefix + "attribute":
+                    # we could distinguish by type; keeping string for now
+                    attribute_keys.append(component.attrib["name"])
+                elif tag == prefix + "sequence":
+                    maxOccurs = component.attrib.get("maxOccurs", "1")
+                    for key in component:
+                        assert key.tag == prefix + "element"
+                        ref = key.attrib["ref"]
+                        keys.append(ref)
+                        if maxOccurs != "1" or key.attrib.get("maxOccurs", "1") != "1":
+                            multiple.append(ref)
+                elif tag == prefix + "simpleContent":
+                    assert len(component) == 1
+                    extension = component[0]
+                    assert extension.tag == prefix + "extension"
+                    assert extension.attrib["base"] == "xs:string"
+                    for attribute in extension:
+                        assert attribute.tag == prefix + "attribute"
+                        # we could distinguish by type; keeping string for now
+                        attribute_keys.append(attribute.attrib["name"])
+                    isSimpleContent = True
+            allowed_tags = frozenset(keys)
+            if len(keys) == 1 and keys == multiple:
+                assert not isSimpleContent
+                args = (allowed_tags,)
+                self.constructors[name] = (ListElement, args)
+            elif len(keys) >= 1:
+                assert not isSimpleContent
+                repeated_tags = frozenset(multiple)
+                args = (allowed_tags, repeated_tags)
+                self.constructors[name] = (DictionaryElement, args)
+            else:
+                self.strings[name] = allowed_tags
+
+    def elementDecl(self, name, model):
+        """Call a call-back function for each element declaration in a DTD.
+
+        This is used for each element declaration in a DTD like::
+
+            <!ELEMENT       name          (...)>
+
+        The purpose of this function is to determine whether this element
+        should be regarded as a string, integer, list, dictionary, structure,
+        or error.
+        """
+        if name.upper() == "ERROR":
+            self.errors.add(name)
+            return
+        if name == "Item" and model == (
+            expat.model.XML_CTYPE_MIXED,
+            expat.model.XML_CQUANT_REP,
+            None,
+            ((expat.model.XML_CTYPE_NAME, expat.model.XML_CQUANT_NONE, "Item", ()),),
+        ):
+            # Special case. As far as I can tell, this only occurs in the
+            # eSummary DTD.
+            self.items.add(name)
+            return
+        # First, remove ignorable parentheses around declarations
+        while (
+            model[0] in (expat.model.XML_CTYPE_SEQ, expat.model.XML_CTYPE_CHOICE)
+            and model[1] in (expat.model.XML_CQUANT_NONE, expat.model.XML_CQUANT_OPT)
+            and len(model[3]) == 1
+        ):
+            model = model[3][0]
+        # PCDATA declarations correspond to strings
+        if model[0] in (expat.model.XML_CTYPE_MIXED, expat.model.XML_CTYPE_EMPTY):
+            if model[1] == expat.model.XML_CQUANT_REP:
+                children = model[3]
+                allowed_tags = frozenset(child[2] for child in children)
+            else:
+                allowed_tags = frozenset()
+            self.strings[name] = allowed_tags
+            return
+        # Children can be anything; use a dictionary-type element
+        if model == (expat.model.XML_CTYPE_ANY, expat.model.XML_CQUANT_NONE, None, ()):
+            allowed_tags = None
+            repeated_tags = None
+            args = (allowed_tags, repeated_tags)
+            self.constructors[name] = (DictionaryElement, args)
+            return
+        # List-type elements
+        if model[0] in (
+            expat.model.XML_CTYPE_CHOICE,
+            expat.model.XML_CTYPE_SEQ,
+        ) and model[1] in (expat.model.XML_CQUANT_PLUS, expat.model.XML_CQUANT_REP):
+            children = model[3]
+            allowed_tags = frozenset(child[2] for child in children)
+            if model[0] == expat.model.XML_CTYPE_SEQ:
+                if len(children) > 1:
+                    assert model[1] == expat.model.XML_CQUANT_PLUS
+                    first_child = children[0]
+                    assert first_child[1] == expat.model.XML_CQUANT_NONE
+                    first_tag = first_child[2]
+                    args = allowed_tags, first_tag
+                    self.constructors[name] = (OrderedListElement, args)
+                    return
+                assert len(children) == 1
+            self.constructors[name] = (ListElement, (allowed_tags,))
+            return
+        # This is the tricky case. Check which keys can occur multiple
+        # times. If only one key is possible, and it can occur multiple
+        # times, then this is a list. If more than one key is possible,
+        # but none of them can occur multiple times, then this is a
+        # dictionary. Otherwise, this is a structure.
+        # In 'single' and 'multiple', we keep track which keys can occur
+        # only once, and which can occur multiple times.
+        single = []
+        multiple = []
+        errors = []
+        # The 'count' function is called recursively to make sure all the
+        # children in this model are counted.
+
+        def count(model):
+            quantifier, key, children = model[1:]
+            if key is None:
+                if quantifier in (
+                    expat.model.XML_CQUANT_PLUS,
+                    expat.model.XML_CQUANT_REP,
+                ):
+                    for child in children:
+                        multiple.append(child[2])
+                else:
+                    for child in children:
+                        count(child)
+            elif key.upper() == "ERROR":
+                errors.append(key)
+            else:
+                if quantifier in (
+                    expat.model.XML_CQUANT_NONE,
+                    expat.model.XML_CQUANT_OPT,
+                ):
+                    single.append(key)
+                elif quantifier in (
+                    expat.model.XML_CQUANT_PLUS,
+                    expat.model.XML_CQUANT_REP,
+                ):
+                    multiple.append(key)
+
+        count(model)
+        if len(single) == 0 and len(multiple) == 1:
+            allowed_tags = frozenset(multiple + errors)
+            self.constructors[name] = (ListElement, (allowed_tags,))
+        else:
+            allowed_tags = frozenset(single + multiple + errors)
+            repeated_tags = frozenset(multiple)
+            args = (allowed_tags, repeated_tags)
+            self.constructors[name] = (DictionaryElement, args)
+
+    def open_dtd_file(self, filename):
+        """Open specified DTD file."""
+        if DataHandler.local_dtd_dir is not None:
+            path = os.path.join(DataHandler.local_dtd_dir, filename)
+            try:
+                handle = open(path, "rb")
+            except FileNotFoundError:
+                pass
+            else:
+                return handle
+        path = os.path.join(DataHandler.global_dtd_dir, filename)
+        try:
+            handle = open(path, "rb")
+        except FileNotFoundError:
+            pass
+        else:
+            return handle
+        return None
+
+    def open_xsd_file(self, filename):
+        """Open specified XSD file."""
+        if DataHandler.local_xsd_dir is not None:
+            path = os.path.join(DataHandler.local_xsd_dir, filename)
+            try:
+                handle = open(path, "rb")
+            except FileNotFoundError:
+                pass
+            else:
+                return handle
+        path = os.path.join(DataHandler.global_xsd_dir, filename)
+        try:
+            handle = open(path, "rb")
+        except FileNotFoundError:
+            pass
+        else:
+            return handle
+        return None
+
+    def save_dtd_file(self, filename, text):
+        """Save DTD file to cache."""
+        if DataHandler.local_dtd_dir is None:
+            return
+        path = os.path.join(DataHandler.local_dtd_dir, filename)
+        try:
+            handle = open(path, "wb")
+        except OSError:
+            warnings.warn(f"Failed to save {filename} at {path}")
+        else:
+            handle.write(text)
+            handle.close()
+
+    def save_xsd_file(self, filename, text):
+        """Save XSD file to cache."""
+        if DataHandler.local_xsd_dir is None:
+            return
+        path = os.path.join(DataHandler.local_xsd_dir, filename)
+        try:
+            handle = open(path, "wb")
+        except OSError:
+            warnings.warn(f"Failed to save {filename} at {path}")
+        else:
+            handle.write(text)
+            handle.close()
+
+    def verify_security(self, url, verify_hostname=True):
+        """Check if the given URL is from a trustable source.
+
+        When ``self.bypass_url_security`` evaluates to ``True``,
+        all URL security checks will be skipped.
+        """
+        if not self.bypass_url_security:
+            parts = urlparse(url)
+            scheme = parts.scheme
+            hostname = parts.hostname
+            if scheme != "https" or (
+                verify_hostname and not hostname.endswith(".nlm.nih.gov")
+            ):
+                raise ValueError(f"Expected secure URL to NCBI, found {url!r}")
+
+    def externalEntityRefHandler(self, context, base, systemId, publicId):
+        """Handle external entity reference in order to cache DTD locally.
+
+        The purpose of this function is to load the DTD locally, instead
+        of downloading it from the URL specified in the XML. Using the local
+        DTD results in much faster parsing. If the DTD is not found locally,
+        we try to download it. If new DTDs become available from NCBI,
+        putting them in Bio/Entrez/DTDs will allow the parser to see them.
+        """
+        urlinfo = urlparse(systemId)
+        if urlinfo.scheme in ["http", "https", "ftp"]:
+            # Then this is an absolute path to the DTD.
+            url = systemId
+        elif urlinfo.scheme == "":
+            # Then this is a relative path to the DTD.
+            # Look at the parent URL to find the full path.
+            try:
+                source = self.dtd_urls[-1]
+            except IndexError:
+                # Assume the default URL for DTDs if the top parent
+                # does not contain an absolute path
+                source = "https://www.ncbi.nlm.nih.gov/dtd/"
+            else:
+                source = os.path.dirname(source)
+            # urls always have a forward slash, don't use os.path.join
+            url = source.rstrip("/") + "/" + systemId
+        else:
+            raise ValueError("Unexpected URL scheme %r" % urlinfo.scheme)
+
+        # NOTE: This trusts any external references from a trusted parent,
+        #       even if these external references go to unknown hosts,
+        #       e.g. when NCBI starts referencing things on a new host
+        #       from existing DTD files.
+        #       Needs to be checked *prior* to appending to ``self.dtd_urls``.
+        self.verify_security(url, verify_hostname=not self.dtd_urls)
+
+        # NOTE: Since ``self.dtd_urls`` being non-empty has security
+        #       consequences with the check above, we use a ``finally`` wrap
+        #       here, in order to guarantee that push and pop are matched.
+        self.dtd_urls.append(url)
+        try:
+            # First, try to load the local version of the DTD file
+            location, filename = os.path.split(systemId)
+            handle = self.open_dtd_file(filename)
+            if not handle:
+                # DTD is not available as a local file. Try accessing it through
+                # the internet instead.
+                try:
+                    handle = urlopen(url)
+                except OSError:
+                    raise RuntimeError(
+                        f"Failed to access {filename} at {url}"
+                    ) from None
+                text = handle.read()
+                handle.close()
+                self.save_dtd_file(filename, text)
+                handle = BytesIO(text)
+
+            parser = self.parser.ExternalEntityParserCreate(context)
+            parser.ElementDeclHandler = self.elementDecl
+            parser.ParseFile(handle)
+            handle.close()
+        finally:
+            self.dtd_urls.pop()
+
+        self.parser.StartElementHandler = self.startElementHandler
+        return 1

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/XSDs/IPGReportSet.xsd

@@ -0,0 +1,97 @@
+<?xml version="1.0" ?>
+<xs:schema
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns:ncbi="http://www.ncbi.nlm.nih.gov"
+  elementFormDefault="unqualified"
+  attributeFormDefault="unqualified"
+>
+  <xs:element name="CDS">
+    <xs:complexType>
+      <xs:attribute name="accver" type="xs:string" use="required"/>
+      <xs:attribute name="kingdom" type="xs:string" use="required"/>
+      <xs:attribute name="kingdom_taxid" type="xs:integer" use="required"/>
+      <xs:attribute name="org" type="xs:string" use="required"/>
+      <xs:attribute name="start" type="xs:integer" use="required"/>
+      <xs:attribute name="stop" type="xs:integer" use="required"/>
+      <xs:attribute name="strand" type="xs:string" use="required"/>
+      <xs:attribute name="strain" type="xs:string" use="optional"/>
+      <xs:attribute name="taxid" type="xs:integer" use="required"/>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="CDSList">
+    <xs:complexType>
+      <xs:sequence maxOccurs="unbounded">
+        <xs:element ref="CDS"/>
+      </xs:sequence>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="IPGReport">
+    <xs:complexType>
+      <xs:sequence>
+        <xs:element ref="Product"/>
+        <xs:element ref="ProteinList"/>
+        <xs:element ref="Statistics"/>
+      </xs:sequence>
+      <xs:attribute name="product_acc" type="xs:string" use="required"/>
+      <xs:attribute name="ipg" type="xs:integer" use="required"/>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="IPGReportSet">
+    <xs:complexType>
+      <xs:sequence>
+        <xs:element ref="IPGReport"/>
+      </xs:sequence>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="Product">
+    <xs:complexType>
+      <xs:simpleContent>
+        <xs:extension base="xs:string">
+          <xs:attribute name="accver" type="xs:string" use="required"/>
+          <xs:attribute name="name" type="xs:string" use="required"/>
+          <xs:attribute name="org" type="xs:string" use="required"/>
+          <xs:attribute name="kingdom" type="xs:string" use="required"/>
+          <xs:attribute name="taxid" type="xs:integer" use="optional"/>
+          <xs:attribute name="slen" type="xs:integer" use="required"/>
+          <xs:attribute name="kingdom_taxid" type="xs:integer" use="required"/>
+        </xs:extension>
+      </xs:simpleContent>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="Protein">
+    <xs:complexType>
+      <xs:sequence minOccurs="0">
+        <xs:element ref="CDSList"/>
+      </xs:sequence>
+      <xs:attribute name="accver" type="xs:string" use="required"/>
+      <xs:attribute name="source" type="xs:string" use="required"/>
+      <xs:attribute name="name" type="xs:string" use="required"/>
+      <xs:attribute name="org" type="xs:string" use="required"/>
+      <xs:attribute name="kingdom" type="xs:string" use="required"/>
+      <xs:attribute name="kingdom_taxid" type="xs:integer" use="required"/>
+      <xs:attribute name="taxid" type="xs:integer" use="optional"/>
+      <xs:attribute name="priority" type="xs:string" use="required"/>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="ProteinList">
+    <xs:complexType>
+      <xs:sequence maxOccurs="unbounded">
+        <xs:element ref="Protein"/>
+      </xs:sequence>
+    </xs:complexType>
+  </xs:element>
+
+  <xs:element name="Statistics">
+    <xs:complexType>
+      <xs:attribute name="nuc_count" type="xs:integer" use="required"/>
+      <xs:attribute name="prot_count" type="xs:integer" use="required"/>
+    </xs:complexType>
+  </xs:element>
+
+</xs:schema>

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd

@@ -0,0 +1,360 @@
+<?xml version="1.0" ?>
+<!-- ============================================
+     ::DATATOOL:: Generated from "blastxml2.asn"
+     ::DATATOOL:: by application DATATOOL version 2.4.4
+     ::DATATOOL:: on 09/23/2015 23:04:21
+     ============================================ -->
+
+<xs:schema
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns:ncbi="http://www.ncbi.nlm.nih.gov"
+  xmlns="http://www.ncbi.nlm.nih.gov"
+  targetNamespace="http://www.ncbi.nlm.nih.gov"
+  elementFormDefault="qualified"
+  attributeFormDefault="unqualified">
+
+<!-- ============================================ -->
+<!-- This section is mapped from module "NCBI-BlastOutput2"
+================================================= -->
+
+
+<xs:element name="BlastOutput2">
+  <xs:complexType>
+    <xs:sequence>
+      <xs:element name="report" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Report"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+      <xs:element name="error" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Err"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="BlastXML2">
+  <xs:complexType>
+    <xs:sequence minOccurs="0" maxOccurs="unbounded">
+      <xs:element ref="BlastOutput2"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Report">
+  <xs:complexType>
+    <xs:sequence>
+<!-- BLAST program: blastp, tblastx etc. -->
+      <xs:element name="program" type="xs:string"/>
+<!-- Program version  -->
+      <xs:element name="version" type="xs:string"/>
+<!-- Steven, David, Tom and others -->
+      <xs:element name="reference" type="xs:string"/>
+      <xs:element name="search-target">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Target"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!-- search parameters -->
+      <xs:element name="params">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Parameters"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+      <xs:element name="results">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Results"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Err">
+  <xs:complexType>
+    <xs:sequence>
+      <xs:element name="code" type="xs:integer"/>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Target">
+  <xs:complexType>
+    <xs:choice>
+<!-- BLAST Database name -->
+      <xs:element name="db" type="xs:string"/>
+<!-- Subject IDs -->
+      <xs:element name="subjects" type="xs:string" maxOccurs="unbounded"/>
+    </xs:choice>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Results">
+  <xs:complexType>
+    <xs:choice>
+      <xs:element name="iterations">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="Iteration"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!--
+  iterative search (psi and delta blast)
+  db search   
+-->
+      <xs:element name="search">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Search"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!--  bl2seq -->
+      <xs:element name="bl2seq">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="Search"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:choice>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Iteration">
+  <xs:complexType>
+    <xs:sequence>
+<!-- iteration number (use with psiblast) -->
+      <xs:element name="iter-num" type="xs:integer"/>
+      <xs:element name="search">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Search"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Search">
+  <xs:complexType>
+    <xs:sequence>
+<!-- SeqId of query -->
+      <xs:element name="query-id" type="xs:string" minOccurs="0"/>
+<!-- Definition line of query -->
+      <xs:element name="query-title" type="xs:string" minOccurs="0"/>
+<!-- length of query sequence -->
+      <xs:element name="query-len" type="xs:integer" minOccurs="0"/>
+<!-- Masked offsets. -->
+      <xs:element name="query-masking" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="Range"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!-- Hits one for every db sequence -->
+      <xs:element name="hits" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="Hit"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!-- search statistics             -->
+      <xs:element name="stat" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element ref="Statistics"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!-- Some (error?) information -->
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Parameters">
+  <xs:complexType>
+    <xs:sequence>
+<!-- Matrix used (-M) -->
+      <xs:element name="matrix" type="xs:string" minOccurs="0"/>
+<!-- Expectation threshold (-e) -->
+      <xs:element name="expect" type="xs:double"/>
+<!-- Inclusion threshold (-h) -->
+      <xs:element name="include" type="xs:double" minOccurs="0"/>
+<!-- match score for NT (-r) -->
+      <xs:element name="sc-match" type="xs:integer" minOccurs="0"/>
+<!-- mismatch score for NT (-q) -->
+      <xs:element name="sc-mismatch" type="xs:integer" minOccurs="0"/>
+<!-- Gap opening cost (-G) -->
+      <xs:element name="gap-open" type="xs:integer" minOccurs="0"/>
+<!-- Gap extension cost (-E) -->
+      <xs:element name="gap-extend" type="xs:integer" minOccurs="0"/>
+<!-- Filtering options (-F) -->
+      <xs:element name="filter" type="xs:string" minOccurs="0"/>
+<!-- PHI-BLAST pattern -->
+      <xs:element name="pattern" type="xs:string" minOccurs="0"/>
+<!-- Limit of request to Entrez query -->
+      <xs:element name="entrez-query" type="xs:string" minOccurs="0"/>
+<!--
+ composition-based stats (numbers correspond to
+ numbering in stand-alone application parameter -comp_based_stats).
+-->
+      <xs:element name="cbs" type="xs:integer" minOccurs="0"/>
+<!-- genetic code for query (blastx or tblastx) -->
+      <xs:element name="query-gencode" type="xs:integer" minOccurs="0"/>
+<!-- genetic code for db or subjects (tblastn or tblastx) -->
+      <xs:element name="db-gencode" type="xs:integer" minOccurs="0"/>
+<!-- bl2seq mode  -->
+      <xs:element name="bl2seq-mode" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<!-- Used to specify start/stop of masking on query. -->
+<xs:element name="Range">
+  <xs:complexType>
+    <xs:sequence>
+<!-- Beginning of masked range (one-offset) -->
+      <xs:element name="from" type="xs:integer"/>
+<!-- End of masked range (one-offset) -->
+      <xs:element name="to" type="xs:integer"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Statistics">
+  <xs:complexType>
+    <xs:sequence>
+<!-- Number of sequences in BLAST db -->
+      <xs:element name="db-num" type="xs:long" minOccurs="0"/>
+<!-- Length of BLAST db -->
+      <xs:element name="db-len" type="xs:long" minOccurs="0"/>
+<!-- Effective HSP length -->
+      <xs:element name="hsp-len" type="xs:integer"/>
+<!-- Effective search space -->
+      <xs:element name="eff-space" type="xs:long"/>
+<!-- Karlin-Altschul parameter K -->
+      <xs:element name="kappa" type="xs:double"/>
+<!-- Karlin-Altschul parameter Lambda -->
+      <xs:element name="lambda" type="xs:double"/>
+<!-- Karlin-Altschul parameter H -->
+      <xs:element name="entropy" type="xs:double"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<!-- Description of entries for this (possibly non-redundant) sequence. -->
+<xs:element name="HitDescr">
+  <xs:complexType>
+    <xs:sequence>
+<!-- SeqId of subject -->
+      <xs:element name="id" type="xs:string"/>
+<!-- accession -->
+      <xs:element name="accession" type="xs:string" minOccurs="0"/>
+<!-- title (definition line) of subject -->
+      <xs:element name="title" type="xs:string" minOccurs="0"/>
+<!-- NCBI taxid (9606 for human) -->
+      <xs:element name="taxid" type="xs:integer" minOccurs="0"/>
+<!-- binomial scientific name ("Homo sapiens" for human).   -->
+      <xs:element name="sciname" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Hit">
+  <xs:complexType>
+    <xs:sequence>
+<!-- hit number -->
+      <xs:element name="num" type="xs:integer"/>
+<!-- ID, title, and taxonomy for each entry in the PIG -->
+      <xs:element name="description">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="HitDescr"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+<!-- length of subject -->
+      <xs:element name="len" type="xs:integer"/>
+<!-- all HSP regions for the given subject -->
+      <xs:element name="hsps" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence minOccurs="0" maxOccurs="unbounded">
+            <xs:element ref="Hsp"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+<xs:element name="Hsp">
+  <xs:complexType>
+    <xs:sequence>
+<!-- HSP number -->
+      <xs:element name="num" type="xs:integer"/>
+<!-- score (in bits) of HSP -->
+      <xs:element name="bit-score" type="xs:double"/>
+<!-- score of HSP -->
+      <xs:element name="score" type="xs:double"/>
+<!-- e-value of HSP -->
+      <xs:element name="evalue" type="xs:double"/>
+<!-- number of identities in HSP -->
+      <xs:element name="identity" type="xs:integer" minOccurs="0"/>
+<!-- number of positives in HSP -->
+      <xs:element name="positive" type="xs:integer" minOccurs="0"/>
+<!-- score density -->
+      <xs:element name="density" type="xs:integer" minOccurs="0"/>
+<!-- start of PHI-BLAST pattern -->
+      <xs:element name="pattern-from" type="xs:integer" minOccurs="0"/>
+<!-- end of PHI-BLAST pattern -->
+      <xs:element name="pattern-to" type="xs:integer" minOccurs="0"/>
+<!-- start of HSP in query -->
+      <xs:element name="query-from" type="xs:integer"/>
+<!-- end of HSP -->
+      <xs:element name="query-to" type="xs:integer"/>
+<!-- Strand of query (blastn) -->
+      <xs:element name="query-strand" type="xs:string" minOccurs="0"/>
+<!-- translation frame of query (blastx, tblastx) -->
+      <xs:element name="query-frame" type="xs:integer" minOccurs="0"/>
+<!-- start of HSP in subject -->
+      <xs:element name="hit-from" type="xs:integer"/>
+<!-- end of HSP in subject -->
+      <xs:element name="hit-to" type="xs:integer"/>
+<!-- Strand of subject (blastn) -->
+      <xs:element name="hit-strand" type="xs:string" minOccurs="0"/>
+<!-- translation frame of subject (tblastn, tblastx) -->
+      <xs:element name="hit-frame" type="xs:integer" minOccurs="0"/>
+<!-- length of the alignment used -->
+      <xs:element name="align-len" type="xs:integer" minOccurs="0"/>
+<!-- number of gaps in HSP -->
+      <xs:element name="gaps" type="xs:integer" minOccurs="0"/>
+<!-- alignment string for the query (with gaps) -->
+      <xs:element name="qseq" type="xs:string"/>
+<!-- alignment string for subject (with gaps) -->
+      <xs:element name="hseq" type="xs:string"/>
+<!-- formating middle line -->
+      <xs:element name="midline" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+</xs:element>
+
+</xs:schema>

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd

@@ -0,0 +1,22 @@
+<?xml version="1.0" ?>
+<!-- ============================================
+     ::DATATOOL:: Generated from "blastxml2.asn"
+     ::DATATOOL:: by application DATATOOL version 2.4.4
+     ::DATATOOL:: on 04/22/2015 11:04:30
+     ============================================ -->
+
+<xs:schema
+  xmlns:xs="http://www.w3.org/2001/XMLSchema"
+  xmlns:ncbi="http://www.ncbi.nlm.nih.gov"
+  xmlns="http://www.ncbi.nlm.nih.gov"
+  targetNamespace="http://www.ncbi.nlm.nih.gov"
+  elementFormDefault="qualified"
+  attributeFormDefault="unqualified">
+
+<!-- NCBI_BlastOutput2.xsd
+  This file is built from a series of basic modules.
+  The actual declarations are in the modules.
+  This file is used to put them together.
+-->
+<xs:include schemaLocation="NCBI_BlastOutput2.mod.xsd"/>
+</xs:schema>

.venv_haddock/lib/python3.12/site-packages/Bio/Entrez/__init__.py

@@ -0,0 +1,747 @@
+# Copyright 1999-2000 by Jeffrey Chang.  All rights reserved.
+# Copyright 2008-2013 by Michiel de Hoon.  All rights reserved.
+# Revisions copyright 2011-2016 by Peter Cock. All rights reserved.
+# Revisions copyright 2015 by Eric Rasche. All rights reserved.
+# Revisions copyright 2015 by Carlos Pena. All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+
+"""Provides code to access NCBI over the WWW.
+
+The main Entrez web page is available at:
+https://www.ncbi.nlm.nih.gov/search/
+
+Entrez Programming Utilities web page is available at:
+https://www.ncbi.nlm.nih.gov/books/NBK25501/
+
+This module provides a number of functions like ``efetch`` (short for
+Entrez Fetch) which will return the data as a handle object. This is
+a standard interface used in Python for reading data from a file, or
+in this case a remote network connection, and provides methods like
+``.read()`` or offers iteration over the contents line by line. See
+also "What the heck is a handle?" in the Biopython Tutorial and
+Cookbook: https://biopython.org/docs/latest/Tutorial/index.html
+
+The handle returned by these functions can be either in text mode or
+in binary mode, depending on the data requested and the results
+returned by NCBI Entrez. Typically, XML data will be in binary mode
+while other data will be in text mode, as required by the downstream
+parser to parse the data.
+
+Unlike a handle to a file on disk from the ``open(filename)`` function,
+which has a ``.name`` attribute giving the filename, the handles from
+``Bio.Entrez`` all have a ``.url`` attribute instead giving the URL
+used to connect to the NCBI Entrez API.
+
+The ``epost``, ``efetch``, and ``esummary`` tools take an "id" parameter
+which corresponds to one or more database UIDs (or accession.version
+identifiers in the case of sequence databases such as "nuccore" or
+"protein"). The Python value of the "id" keyword passed to these functions
+may be either a single ID as a string or integer or multiple IDs as an
+iterable of strings/integers. You may also pass a single string containing
+multiple IDs delimited by commas. The ``elink`` tool also accepts multiple
+IDs but the argument is handled differently than the other three. See that
+function's docstring for more information.
+
+All the functions that send requests to the NCBI Entrez API will
+automatically respect the NCBI rate limit (of 3 requests per second
+without an API key, or 10 requests per second with an API key) and
+will automatically retry when encountering transient failures
+(i.e. connection failures or HTTP 5XX codes). By default, Biopython
+does a maximum of three tries before giving up, and sleeps for 15
+seconds between tries. You can tweak these parameters by setting
+``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.
+
+The Entrez module also provides an XML parser which takes a handle
+as input.
+
+Variables:
+
+    - email        Set the Entrez email parameter (default is not set).
+    - tool         Set the Entrez tool parameter (default is ``biopython``).
+    - api_key      Personal API key from NCBI. If not set, only 3 queries per
+      second are allowed. 10 queries per seconds otherwise with a
+      valid API key.
+    - max_tries    Configures how many times failed requests will be
+      automatically retried on error (default is 3).
+    - sleep_between_tries   The delay, in seconds, before retrying a request on
+      error (default is 15).
+
+Functions:
+
+    - efetch       Retrieves records in the requested format from a list of one or
+      more primary IDs or from the user's environment
+    - epost        Posts a file containing a list of primary IDs for future use in
+      the user's environment to use with subsequent search strategies
+    - esearch      Searches and retrieves primary IDs (for use in EFetch, ELink,
+      and ESummary) and term translations and optionally retains
+      results for future use in the user's environment.
+    - elink        Checks for the existence of an external or Related Articles link
+      from a list of one or more primary IDs.  Retrieves primary IDs
+      and relevancy scores for links to Entrez databases or Related
+      Articles;  creates a hyperlink to the primary LinkOut provider
+      for a specific ID and database, or lists LinkOut URLs
+      and Attributes for multiple IDs.
+    - einfo        Provides field index term counts, last update, and available
+      links for each database.
+    - esummary     Retrieves document summaries from a list of primary IDs or from
+      the user's environment.
+    - egquery      Provides Entrez database counts in XML for a single search
+      using Global Query.
+    - espell       Retrieves spelling suggestions.
+    - ecitmatch    Retrieves PubMed IDs (PMIDs) that correspond to a set of
+      input citation strings.
+
+    - read         Parses the XML results returned by any of the above functions.
+      Alternatively, the XML data can be read from a file opened in binary mode.
+      Typical usage is:
+
+          >>> from Bio import Entrez
+          >>> Entrez.email = "Your.Name.Here@example.org"
+          >>> handle = Entrez.einfo() # or esearch, efetch, ...
+          >>> record = Entrez.read(handle)
+          >>> handle.close()
+
+       where record is now a Python dictionary or list.
+
+    - parse        Parses the XML results returned by those of the above functions
+      which can return multiple records - such as efetch, esummary
+      and elink. Typical usage is:
+
+          >>> handle = Entrez.efetch(db="taxonomy", id="9615,9685", retmode="xml")
+          >>> records = Entrez.parse(handle)
+          >>> for record in records:
+          ...     print(record['TaxId'], record["OtherNames"]['GenbankCommonName'])
+          ...
+          9615 dog
+          9685 domestic cat
+          >>> handle.close()
+
+      This function is appropriate only if the XML file contains
+      multiple records, and is particular useful for large files.
+
+    - _open        Internally used function.
+
+"""
+
+import io
+import time
+import warnings
+from urllib.error import HTTPError
+from urllib.error import URLError
+from urllib.parse import urlencode
+from urllib.request import Request
+from urllib.request import urlopen
+
+from Bio._utils import function_with_previous
+
+email = None
+max_tries = 3
+sleep_between_tries = 15
+tool = "biopython"
+api_key = None
+local_cache = None
+
+
+# XXX retmode?
+def epost(db, **keywds):
+    """Post a file of identifiers for future use.
+
+    Posts a file containing a list of UIs for future use in the user's
+    environment to use with subsequent search strategies.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EPost
+
+    :returns: Handle to the results.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi"
+    variables = {"db": db}
+    variables.update(keywds)
+    request = _build_request(cgi, variables, post=True)
+    return _open(request)
+
+
+def efetch(db, **keywords):
+    """Fetch Entrez results which are returned as a handle.
+
+    EFetch retrieves records in the requested format from a list or set of one or
+    more UIs or from user's environment.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
+
+    Short example:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> handle = Entrez.efetch(db="nucleotide", id="AY851612", rettype="gb", retmode="text")
+    >>> print(handle.readline().strip())
+    LOCUS       AY851612                 892 bp    DNA     linear   PLN 10-APR-2007
+    >>> handle.close()
+
+    This will automatically use an HTTP POST rather than HTTP GET if there
+    are over 200 identifiers as recommended by the NCBI.
+
+    **Warning:** The NCBI changed the default retmode in Feb 2012, so many
+    databases which previously returned text output now give XML.
+
+    :returns: Handle to the results.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
+    variables = {"db": db}
+    variables.update(keywords)
+    request = _build_request(cgi, variables)
+    return _open(request)
+
+
+def esearch(db, term, **keywds):
+    """Run an Entrez search and return a handle to the results.
+
+    ESearch searches and retrieves primary IDs (for use in EFetch, ELink
+    and ESummary) and term translations, and optionally retains results
+    for future use in the user's environment.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
+
+    Short example:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> handle = Entrez.esearch(
+    ...     db="nucleotide", retmax=10, idtype="acc",
+    ...     term="opuntia[ORGN] accD 2007[Publication Date]"
+    ... )
+    ...
+    >>> record = Entrez.read(handle)
+    >>> handle.close()
+    >>> int(record["Count"]) >= 2
+    True
+    >>> "EF590893.1" in record["IdList"]
+    True
+    >>> "EF590892.1" in record["IdList"]
+    True
+
+    :returns: Handle to the results, which are always in XML format.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+    variables = {"db": db, "term": term}
+    variables.update(keywds)
+    request = _build_request(cgi, variables)
+    return _open(request)
+
+
+def elink(**keywds):
+    """Check for linked external articles and return a handle.
+
+    ELink checks for the existence of an external or Related Articles link
+    from a list of one or more primary IDs;  retrieves IDs and relevancy
+    scores for links to Entrez databases or Related Articles; creates a
+    hyperlink to the primary LinkOut provider for a specific ID and
+    database, or lists LinkOut URLs and attributes for multiple IDs.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ELink
+
+    Note that ELink treats the "id" parameter differently than the other
+    tools when multiple values are given. You should generally pass multiple
+    UIDs as a list of strings or integers. This will provide a "one-to-one"
+    mapping from source database UIDs to destination database UIDs in the
+    result. If multiple source UIDs are passed as a single comma-delimited
+    string all destination UIDs will be mixed together in the result.
+
+    This example finds articles related to the Biopython application
+    note's entry in the PubMed database:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> pmid = "19304878"
+    >>> handle = Entrez.elink(dbfrom="pubmed", id=pmid, linkname="pubmed_pubmed")
+    >>> record = Entrez.read(handle)
+    >>> handle.close()
+    >>> print(record[0]["LinkSetDb"][0]["LinkName"])
+    pubmed_pubmed
+    >>> linked = [link["Id"] for link in record[0]["LinkSetDb"][0]["Link"]]
+    >>> "14630660" in linked
+    True
+
+    This is explained in much more detail in the Biopython Tutorial.
+
+    :returns: Handle to the results, by default in XML format.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
+    variables = {}
+    variables.update(keywds)
+    request = _build_request(cgi, variables, join_ids=False)
+    return _open(request)
+
+
+def einfo(**keywds):
+    """Return a summary of the Entrez databases as a results handle.
+
+    EInfo provides field names, index term counts, last update, and
+    available links for each Entrez database.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo
+
+    Short example:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> record = Entrez.read(Entrez.einfo())
+    >>> 'pubmed' in record['DbList']
+    True
+
+    :returns: Handle to the results, by default in XML format.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"
+    variables = {}
+    variables.update(keywds)
+    request = _build_request(cgi, variables)
+    return _open(request)
+
+
+def esummary(**keywds):
+    """Retrieve document summaries as a results handle.
+
+    ESummary retrieves document summaries from a list of primary IDs or
+    from the user's environment.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESummary
+
+    This example discovers more about entry 19923 in the structure
+    database:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> handle = Entrez.esummary(db="structure", id="19923")
+    >>> record = Entrez.read(handle)
+    >>> handle.close()
+    >>> print(record[0]["Id"])
+    19923
+    >>> print(record[0]["PdbDescr"])
+    CRYSTAL STRUCTURE OF E. COLI ACONITASE B
+
+
+    :returns: Handle to the results, by default in XML format.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
+    variables = {}
+    variables.update(keywds)
+    request = _build_request(cgi, variables)
+    return _open(request)
+
+
+def espell(**keywds):
+    """Retrieve spelling suggestions as a results handle.
+
+    ESpell retrieves spelling suggestions, if available.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESpell
+
+    Short example:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> record = Entrez.read(Entrez.espell(term="biopythooon"))
+    >>> print(record["Query"])
+    biopythooon
+    >>> print(record["CorrectedQuery"])
+    biopython
+
+    :returns: Handle to the results, by default in XML format.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi"
+    variables = {}
+    variables.update(keywds)
+    request = _build_request(cgi, variables)
+    return _open(request)
+
+
+def _update_ecitmatch_variables(keywds):
+    # XML is the only supported value, and it actually returns TXT.
+    variables = {"retmode": "xml"}
+    citation_keys = (
+        "journal_title",
+        "year",
+        "volume",
+        "first_page",
+        "author_name",
+        "key",
+    )
+
+    # Accept pre-formatted strings
+    if isinstance(keywds["bdata"], str):
+        variables.update(keywds)
+    else:
+        # Alternatively accept a nicer interface
+        variables["db"] = keywds["db"]
+        bdata = []
+        for citation in keywds["bdata"]:
+            formatted_citation = "|".join(
+                [citation.get(key, "") for key in citation_keys]
+            )
+            bdata.append(formatted_citation)
+        variables["bdata"] = "\r".join(bdata)
+    return variables
+
+
+def ecitmatch(**keywds):
+    """Retrieve PMIDs for input citation strings, returned as a handle.
+
+    ECitMatch retrieves PubMed IDs (PMIDs) that correspond to a set of input
+    citation strings.
+
+    See the online documentation for an explanation of the parameters:
+    https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ECitMatch
+
+    Short example:
+
+    >>> from Bio import Entrez
+    >>> Entrez.email = "Your.Name.Here@example.org"
+    >>> citation_1 = {"journal_title": "proc natl acad sci u s a",
+    ...               "year": "1991", "volume": "88", "first_page": "3248",
+    ...               "author_name": "mann bj", "key": "citation_1"}
+    >>> handle = Entrez.ecitmatch(db="pubmed", bdata=[citation_1])
+    >>> print(handle.read().strip().split("|"))
+    ['proc natl acad sci u s a', '1991', '88', '3248', 'mann bj', 'citation_1', '2014248']
+    >>> handle.close()
+
+    :returns: Handle to the results, by default in plain text.
+    :raises urllib.error.URLError: If there's a network error.
+    """
+    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi"
+    variables = _update_ecitmatch_variables(keywds)
+    request = _build_request(cgi, variables, ecitmatch=True)
+    return _open(request)
+
+
+def read(source, validate=True, escape=False, ignore_errors=False):
+    """Parse an XML file from the NCBI Entrez Utilities into python objects.
+
+    This function parses an XML file created by NCBI's Entrez Utilities,
+    returning a multilevel data structure of Python lists and dictionaries.
+    Most XML files returned by NCBI's Entrez Utilities can be parsed by
+    this function, provided its DTD is available. Biopython includes the
+    DTDs for most commonly used Entrez Utilities.
+
+    The argument ``source`` must be a file or file-like object opened in binary
+    mode, or a filename. The parser detects the encoding from the XML file, and
+    uses it to convert all text in the XML to the correct Unicode string. The
+    functions in Bio.Entrez to access NCBI Entrez will automatically return XML
+    data in binary mode. For files, use mode "rb" when opening the file, as in
+
+        >>> from Bio import Entrez
+        >>> path = "Entrez/esearch1.xml"
+        >>> stream = open(path, "rb")  # opened in binary mode
+        >>> record = Entrez.read(stream)
+        >>> print(record['QueryTranslation'])
+        "biopython"[All Fields]
+        >>> stream.close()
+
+    Alternatively, you can use the filename directly, as in
+
+        >>> record = Entrez.read(path)
+        >>> print(record['QueryTranslation'])
+        "biopython"[All Fields]
+
+    which is safer, as the file stream will automatically be closed after the
+    record has been read, or if an error occurs.
+
+    If validate is True (default), the parser will validate the XML file
+    against the DTD, and raise an error if the XML file contains tags that
+    are not represented in the DTD. If validate is False, the parser will
+    simply skip such tags.
+
+    If escape is True, all characters that are not valid HTML are replaced
+    by HTML escape characters to guarantee that the returned strings are
+    valid HTML fragments. For example, a less-than sign (<) is replaced by
+    &lt;. If escape is False (default), the string is returned as is.
+
+    If ignore_errors is False (default), any error messages in the XML file
+    will raise a RuntimeError. If ignore_errors is True, error messages will
+    be stored as ErrorElement items, without raising an exception.
+
+    Whereas the data structure seems to consist of generic Python lists,
+    dictionaries, strings, and so on, each of these is actually a class
+    derived from the base type. This allows us to store the attributes
+    (if any) of each element in a dictionary my_element.attributes, and
+    the tag name in my_element.tag.
+    """
+    from .Parser import DataHandler
+
+    handler = DataHandler(validate, escape, ignore_errors)
+    record = handler.read(source)
+    return record
+
+
+def parse(source, validate=True, escape=False, ignore_errors=False):
+    """Parse an XML file from the NCBI Entrez Utilities into python objects.
+
+    This function parses an XML file created by NCBI's Entrez Utilities,
+    returning a multilevel data structure of Python lists and dictionaries.
+    This function is suitable for XML files that (in Python) can be represented
+    as a list of individual records. Whereas 'read' reads the complete file
+    and returns a single Python list, 'parse' is a generator function that
+    returns the records one by one. This function is therefore particularly
+    useful for parsing large files.
+
+    Most XML files returned by NCBI's Entrez Utilities can be parsed by
+    this function, provided its DTD is available. Biopython includes the
+    DTDs for most commonly used Entrez Utilities.
+
+    The argument ``source`` must be a file or file-like object opened in binary
+    mode, or a filename. The parser detects the encoding from the XML file, and
+    uses it to convert all text in the XML to the correct Unicode string. The
+    functions in Bio.Entrez to access NCBI Entrez will automatically return XML
+    data in binary mode. For files, use mode "rb" when opening the file, as in
+
+        >>> from Bio import Entrez
+        >>> path = "Entrez/taxonomy.xml"
+        >>> stream = open(path, "rb")  # opened in binary mode
+        >>> records = Entrez.parse(stream)
+        >>> for record in records:
+        ...     print(record['TaxId'], record["OtherNames"]['GenbankCommonName'])
+        ...
+        9615 dog
+        9685 domestic cat
+        >>> stream.close()
+
+    Alternatively, you can use the filename directly, as in
+
+        >>> records = Entrez.parse(path)
+        >>> for record in records:
+        ...     print(record['TaxId'], record["OtherNames"]['GenbankCommonName'])
+        ...
+        9615 dog
+        9685 domestic cat
+
+    which is safer, as the file stream will automatically be closed after all
+    the records have been read, or if an error occurs.
+
+    If validate is True (default), the parser will validate the XML file
+    against the DTD, and raise an error if the XML file contains tags that
+    are not represented in the DTD. If validate is False, the parser will
+    simply skip such tags.
+
+    If escape is True, all characters that are not valid HTML are replaced
+    by HTML escape characters to guarantee that the returned strings are
+    valid HTML fragments. For example, a less-than sign (<) is replaced by
+    &lt;. If escape is False (default), the string is returned as is.
+
+    If ignore_errors is False (default), any error messages in the XML file
+    will raise a RuntimeError. If ignore_errors is True, error messages will
+    be stored as ErrorElement items, without raising an exception.
+
+    Whereas the data structure seems to consist of generic Python lists,
+    dictionaries, strings, and so on, each of these is actually a class
+    derived from the base type. This allows us to store the attributes
+    (if any) of each element in a dictionary my_element.attributes, and
+    the tag name in my_element.tag.
+    """
+    from .Parser import DataHandler
+
+    handler = DataHandler(validate, escape, ignore_errors)
+    records = handler.parse(source)
+    return records
+
+
+@function_with_previous
+def _open(request):
+    """Make an HTTP request to Entrez, handling errors and enforcing rate limiting (PRIVATE).
+
+    Does some simple error checking and will try again after certain types of errors, up to
+    ``max_retries`` times. This function also enforces the "up to three queries per second
+    rule" to avoid abusing the NCBI servers (this limit is increased to 10 if using an API key).
+
+    :param req_or_cgi: A Request object returned by ``_build_request``.
+    :type req_or_cgi: urllib.request.Request
+    :returns: Handle to HTTP response as returned by ``urllib.request.urlopen``. Will be wrapped in
+        an ``io.TextIOWrapper`` if its content type is plain text.
+    :rtype: http.client.HTTPResponse or io.TextIOWrapper
+    :raises urllib.error.URLError: Errors raised by ``urlopen`` past the maximum number of retries.
+    """
+    # NCBI requirement: At most three queries per second if no API key is provided.
+    # Equivalently, at least a third of second between queries
+    # Using just 0.333333334 seconds sometimes hit the NCBI rate limit,
+    # the slightly longer pause of 0.37 seconds has been more reliable.
+    delay = 0.1 if _has_api_key(request) else 0.37
+    current = time.time()
+    wait = _open.previous + delay - current
+    if wait > 0:
+        time.sleep(wait)
+        _open.previous = current + wait
+    else:
+        _open.previous = current
+
+    for i in range(max_tries):
+        try:
+            handle = urlopen(request)
+        except HTTPError as exception:
+            # Reraise if the final try fails
+            if i >= max_tries - 1:
+                raise
+            # Reraise if the exception is triggered by a HTTP 4XX error
+            # indicating some kind of bad request, UNLESS it's specifically a
+            # 429 "Too Many Requests" response. NCBI seems to sometimes
+            # erroneously return 429s even when their rate limit is
+            # honored (and indeed even with the rate-limit-related fudging
+            # higher up in this function in place), so the best we can do is
+            # treat them as a serverside error and try again after sleeping
+            # for a bit.
+            if exception.code // 100 == 4 and exception.code != 429:
+                raise
+        except URLError:
+            # Reraise if the final try fails
+            if i >= max_tries - 1:
+                raise
+            # Treat as a transient error and try again after a brief delay:
+            time.sleep(sleep_between_tries)
+        else:
+            break
+
+    subtype = handle.headers.get_content_subtype()
+    if subtype == "plain":
+        url = handle.url
+        handle = io.TextIOWrapper(handle, encoding="UTF-8")
+        handle.url = url
+    return handle
+
+
+_open.previous = 0
+
+
+def _build_request(cgi, params=None, post=None, ecitmatch=False, join_ids=True):
+    """Build a Request object for an E-utility.
+
+    :param str cgi: base URL for the CGI script to access.
+    :param params: Mapping containing options to pass to the CGI script. Keys must be strings.
+    :type params: dict or None
+    :param bool post: Whether to use the HTTP POST method rather than GET. By default (``post=None``),
+        POST is used if the URL encoded parameters would be over 1000 characters long, as is
+        suggested in the E-Utilities documentation.
+    :param bool ecitmatch: Don't URL-encode pipe ("|") characters, this is expected by the ecitmatch
+        tool.
+    :param bool join_ids: Passed to ``_construct_params``.
+    :returns: A request object ready to be passed to ``_open``.
+    :rtype: urllib.request.Request
+    """
+    params = _construct_params(params, join_ids=join_ids)
+
+    params_str = urlencode(params, doseq=True)
+    if ecitmatch:
+        params_str = params_str.replace("%7C", "|")
+
+    # By default, post is None. Set to a boolean to over-ride length choice:
+    if post is None and len(params_str) > 1000:
+        post = True
+
+    # NCBI prefers an HTTP POST instead of an HTTP GET if there are more than about 200 IDs
+    if post is None and "id" in params:
+        idcount = params["id"].count(",") + 1
+        if idcount >= 200:
+            post = True
+
+    if post:
+        return Request(cgi, data=params_str.encode("utf8"), method="POST")
+    else:
+        return Request(cgi + "?" + params_str, method="GET")
+
+
+def _construct_params(params, join_ids=True):
+    """Construct/format parameter dict for an Entrez request.
+
+    :param params: User-supplied parameters.
+    :type params: dict or None
+    :param bool join_ids: If True and the "id" key of ``params`` is a list
+        containing multiple UIDs, join them into a single comma-delimited string.
+    :returns: Parameters with defaults added and keys with None values removed.
+    :rtype: dict
+    """
+    if params is None:
+        params = {}
+
+    # Tell Entrez that we are using Biopython (or whatever the user has
+    # specified explicitly in the parameters or by changing the default)
+    params.setdefault("tool", tool)
+
+    # Tell Entrez who we are
+    params.setdefault("email", email)
+    params.setdefault("api_key", api_key)
+
+    # Remove None values from the parameters
+    for key, value in list(params.items()):
+        if value is None:
+            del params[key]
+
+    # Warn if email not set
+    if "email" not in params:
+        warnings.warn(
+            """
+            Email address is not specified.
+
+            To make use of NCBI's E-utilities, NCBI requires you to specify your
+            email address with each request.  As an example, if your email address
+            is A.N.Other@example.com, you can specify it as follows:
+               from Bio import Entrez
+               Entrez.email = 'A.N.Other@example.com'
+            In case of excessive usage of the E-utilities, NCBI will attempt to contact
+            a user at the email address provided before blocking access to the
+            E-utilities.""",
+            UserWarning,
+        )
+
+    # Format "id" parameter properly
+    if join_ids and "id" in params:
+        params["id"] = _format_ids(params["id"])
+
+    return params
+
+
+def _format_ids(ids):
+    """Convert one or more UIDs to a single comma-delimited string.
+
+    Input may be a single ID as an integer or string, an iterable of strings/ints,
+    or a string of IDs already separated by commas.
+    """
+    if isinstance(ids, int):
+        # Single integer, just convert to str
+        return str(ids)
+
+    if isinstance(ids, str):
+        # String which represents one or more IDs joined by commas
+        # Remove any whitespace around commas if they are present
+        return ",".join(id.strip() for id in ids.split(","))
+
+    # Not a string or integer, assume iterable
+    return ",".join(map(str, ids))
+
+
+def _has_api_key(request):
+    """Check if a Request has the api_key parameter set, to set the rate limit.
+
+    Works with GET or POST requests.
+    """
+    if request.method == "POST":
+        return b"api_key=" in request.data
+    return "api_key=" in request.full_url
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/Enzyme.py

@@ -0,0 +1,159 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# Copyright 2009 by Michiel de Hoon.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Parse the enzyme.dat file from Enzyme at ExPASy.
+
+See https://www.expasy.org/enzyme/
+
+Tested with the release of 03-Mar-2009.
+
+Functions:
+ - read       Reads a file containing one ENZYME entry
+ - parse      Reads a file containing multiple ENZYME entries
+
+Classes:
+ - Record     Holds ENZYME data.
+
+"""
+
+
+def parse(handle):
+    """Parse ENZYME records.
+
+    This function is for parsing ENZYME files containing multiple
+    records.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    while True:
+        record = __read(handle)
+        if not record:
+            break
+        yield record
+
+
+def read(handle):
+    """Read one ENZYME record.
+
+    This function is for parsing ENZYME files containing
+    exactly one record.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    record = __read(handle)
+    # We should have reached the end of the record by now
+    remainder = handle.read()
+    if remainder:
+        raise ValueError("More than one ENZYME record found")
+    return record
+
+
+class Record(dict):
+    """Holds information from an ExPASy ENZYME record as a Python dictionary.
+
+    Each record contains the following keys:
+
+    - ID: EC number
+    - DE: Recommended name
+    - AN: Alternative names (if any)
+    - CA: Catalytic activity
+    - CF: Cofactors (if any)
+    - PR: Pointers to any Prosite documentation entries that correspond to the
+      enzyme
+    - DR: Pointers to any Swiss-Prot protein sequence entries that correspond
+      to the enzyme
+    - CC: Comments
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        dict.__init__(self)
+        self["ID"] = ""
+        self["DE"] = ""
+        self["AN"] = []
+        self["CA"] = ""
+        self["CF"] = ""
+        self["CC"] = []  # one comment per line
+        self["PR"] = []
+        self["DR"] = []
+
+    def __repr__(self):
+        """Return the canonical string representation of the Record object."""
+        if self["ID"]:
+            if self["DE"]:
+                return f"{self.__class__.__name__} ({self['ID']}, {self['DE']})"
+            else:
+                return f"{self.__class__.__name__} ({self['ID']})"
+        else:
+            return f"{self.__class__.__name__} ( )"
+
+    def __str__(self):
+        """Return a readable string representation of the Record object."""
+        output = [
+            "ID: " + self["ID"],
+            "DE: " + self["DE"],
+            "AN: " + repr(self["AN"]),
+            "CA: '" + self["CA"] + "'",
+            "CF: " + self["CF"],
+            "CC: " + repr(self["CC"]),
+            "PR: " + repr(self["PR"]),
+            "DR: %d Records" % len(self["DR"]),
+        ]
+        return "\n".join(output)
+
+
+# Everything below is private
+
+
+def __read(handle):
+    record = None
+    for line in handle:
+        key, value = line[:2], line[5:].rstrip()
+        if key == "ID":
+            record = Record()
+            record["ID"] = value
+        elif key == "DE":
+            record["DE"] += value
+        elif key == "AN":
+            if record["AN"] and not record["AN"][-1].endswith("."):
+                record["AN"][-1] += " " + value
+            else:
+                record["AN"].append(value)
+        elif key == "CA":
+            record["CA"] += value
+        elif key == "DR":
+            pair_data = value.rstrip(";").split(";")
+            for pair in pair_data:
+                t1, t2 = pair.split(",")
+                row = [t1.strip(), t2.strip()]
+                record["DR"].append(row)
+        elif key == "CF":
+            if record["CF"]:
+                record["CF"] += " " + value
+            else:
+                record["CF"] = value
+        elif key == "PR":
+            assert value.startswith("PROSITE; ")
+            value = value[9:].rstrip(";")
+            record["PR"].append(value)
+        elif key == "CC":
+            if value.startswith("-!- "):
+                record["CC"].append(value[4:])
+            elif value.startswith("    ") and record["CC"]:
+                record["CC"][-1] += value[3:]
+            # copyright notice is silently skipped
+        elif key == "//":
+            if record:
+                return record
+            else:  # This was the copyright notice
+                continue
+    if record:
+        raise ValueError("Unexpected end of stream")

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/Prodoc.py

@@ -0,0 +1,173 @@
+# Copyright 2000 by Jeffrey Chang.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code to work with the prosite.doc file from Prosite.
+
+See https://www.expasy.org/prosite/
+
+Tested with:
+ - Release 15.0, July 1998
+ - Release 16.0, July 1999
+ - Release 20.22, 13 November 2007
+ - Release 20.43, 10 February 2009
+
+Functions:
+ - read               Read a Prodoc file containing exactly one Prodoc entry.
+ - parse              Iterates over entries in a Prodoc file.
+
+Classes:
+ - Record             Holds Prodoc data.
+ - Reference          Holds data from a Prodoc reference.
+
+"""
+
+
+def read(handle):
+    """Read in a record from a file with exactly one Prodoc record."""
+    record = __read(handle)
+    # We should have reached the end of the record by now
+    line = handle.readline()
+    if line:
+        raise ValueError("More than one Prodoc record found")
+    return record
+
+
+def parse(handle):
+    """Iterate over the records in a Prodoc file."""
+    while True:
+        record = __read(handle)
+        if not record:
+            return
+        yield record
+
+
+class Record:
+    """Holds information from a Prodoc record.
+
+    Attributes:
+     - accession      Accession number of the record.
+     - prosite_refs   List of tuples (prosite accession, prosite name).
+     - text           Free format text.
+     - references     List of reference objects.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.accession = ""
+        self.prosite_refs = []
+        self.text = ""
+        self.references = []
+
+
+class Reference:
+    """Holds information from a Prodoc citation.
+
+    Attributes:
+     - number     Number of the reference. (string)
+     - authors    Names of the authors.
+     - citation   Describes the citation.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.number = ""
+        self.authors = ""
+        self.citation = ""
+
+
+# Below are private functions
+
+
+def __read_prosite_reference_line(record, line):
+    line = line.rstrip()
+    if line[-1] != "}":
+        raise ValueError(f"I don't understand the Prosite reference on line\n{line}")
+    acc, name = line[1:-1].split("; ")
+    record.prosite_refs.append((acc, name))
+
+
+def __read_text_line(record, line):
+    record.text += line
+    return True
+
+
+def __read_reference_start(record, line):
+    # Read the references
+    reference = Reference()
+    reference.number = line[1:3].strip()
+    if line[1] == "E":
+        # If it's an electronic reference, then the URL is on the
+        # line, instead of the author.
+        reference.citation = line[4:].strip()
+    else:
+        reference.authors = line[4:].strip()
+    record.references.append(reference)
+
+
+def __read_reference_line(record, line):
+    if not line.strip():
+        return False
+    reference = record.references[-1]
+    if line.startswith("     "):
+        if reference.authors[-1] == ",":
+            reference.authors += line[4:].rstrip()
+        else:
+            reference.citation += line[5:]
+        return True
+    raise Exception(f"I don't understand the reference line\n{line}")
+
+
+def __read_copyright_line(record, line):
+    # Skip the copyright statement
+    if line.startswith("+----"):
+        return False
+    return True
+
+
+def __read(handle):
+    # Skip blank lines between records
+    for line in handle:
+        line = line.rstrip()
+        if line and not line.startswith("//"):
+            break
+    else:
+        return None
+    record = Record()
+    # Read the accession number
+    if not line.startswith("{PDOC"):
+        raise ValueError("Line does not start with '{PDOC':\n%s" % line)
+    if line[-1] != "}":
+        raise ValueError(f"I don't understand accession line\n{line}")
+    record.accession = line[1:-1]
+    # Read the Prosite references
+    for line in handle:
+        if line.startswith("{PS"):
+            __read_prosite_reference_line(record, line)
+        else:
+            break
+    else:
+        raise ValueError("Unexpected end of stream.")
+    # Read the actual text
+    if not line.startswith("{BEGIN"):
+        raise ValueError("Line does not start with '{BEGIN':\n%s" % line)
+    read_line = __read_text_line
+    for line in handle:
+        if line.startswith("{END}"):
+            # Clean up the record and return
+            for reference in record.references:
+                reference.citation = reference.citation.rstrip()
+                reference.authors = reference.authors.rstrip()
+            return record
+        elif line[0] == "[" and line[3] == "]" and line[4] == " ":
+            __read_reference_start(record, line)
+            read_line = __read_reference_line
+        elif line.startswith("+----"):
+            read_line = __read_copyright_line
+        elif read_line:
+            if not read_line(record, line):
+                read_line = None
+    raise ValueError("Unexpected end of stream.")

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/Prosite.py

@@ -0,0 +1,308 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# Copyright 2000 by Jeffrey Chang.  All rights reserved.
+# Revisions Copyright 2007 by Peter Cock.  All rights reserved.
+# Revisions Copyright 2009 by Michiel de Hoon.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+"""Parser for the prosite dat file from Prosite at ExPASy.
+
+See https://www.expasy.org/prosite/
+
+Tested with:
+ - Release 20.43, 10-Feb-2009
+ - Release 2017_03 of 15-Mar-2017.
+
+Functions:
+ - read                  Reads a Prosite file containing one Prosite record
+ - parse                 Iterates over records in a Prosite file.
+
+Classes:
+ - Record                Holds Prosite data.
+
+"""
+
+
+def parse(handle):
+    """Parse Prosite records.
+
+    This function is for parsing Prosite files containing multiple
+    records.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    while True:
+        record = __read(handle)
+        if not record:
+            break
+        yield record
+
+
+def read(handle):
+    """Read one Prosite record.
+
+    This function is for parsing Prosite files containing
+    exactly one record.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    record = __read(handle)
+    # We should have reached the end of the record by now
+    remainder = handle.read()
+    if remainder:
+        raise ValueError("More than one Prosite record found")
+    return record
+
+
+class Record:
+    """Holds information from a Prosite record.
+
+    Main attributes:
+     - name           ID of the record.  e.g. ADH_ZINC
+     - type           Type of entry.  e.g. PATTERN, MATRIX, or RULE
+     - accession      e.g. PS00387
+     - created        Date the entry was created.  (MMM-YYYY for releases
+       before January 2017, DD-MMM-YYYY since January 2017)
+     - data_update    Date the 'primary' data was last updated.
+     - info_update    Date data other than 'primary' data was last updated.
+     - pdoc           ID of the PROSITE DOCumentation.
+     - description    Free-format description.
+     - pattern        The PROSITE pattern.  See docs.
+     - matrix         List of strings that describes a matrix entry.
+     - rules          List of rule definitions (from RU lines).  (strings)
+     - prorules       List of prorules (from PR lines). (strings)
+
+    NUMERICAL RESULTS:
+     - nr_sp_release  SwissProt release.
+     - nr_sp_seqs     Number of seqs in that release of Swiss-Prot. (int)
+     - nr_total       Number of hits in Swiss-Prot.  tuple of (hits, seqs)
+     - nr_positive    True positives.  tuple of (hits, seqs)
+     - nr_unknown     Could be positives.  tuple of (hits, seqs)
+     - nr_false_pos   False positives.  tuple of (hits, seqs)
+     - nr_false_neg   False negatives.  (int)
+     - nr_partial     False negatives, because they are fragments. (int)
+
+    COMMENTS:
+     - cc_taxo_range  Taxonomic range.  See docs for format
+     - cc_max_repeat  Maximum number of repetitions in a protein
+     - cc_site        Interesting site.  list of tuples (pattern pos, desc.)
+     - cc_skip_flag   Can this entry be ignored?
+     - cc_matrix_type
+     - cc_scaling_db
+     - cc_author
+     - cc_ft_key
+     - cc_ft_desc
+     - cc_version     version number (introduced in release 19.0)
+
+    The following are all lists if tuples (swiss-prot accession, swiss-prot name).
+
+    DATA BANK REFERENCES:
+     - dr_positive
+     - dr_false_neg
+     - dr_false_pos
+     - dr_potential   Potential hits, but fingerprint region not yet available.
+     - dr_unknown     Could possibly belong
+     - pdb_structs    List of PDB entries.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.name = ""
+        self.type = ""
+        self.accession = ""
+        self.created = ""
+        self.data_update = ""
+        self.info_update = ""
+        self.pdoc = ""
+
+        self.description = ""
+        self.pattern = ""
+        self.matrix = []
+        self.rules = []
+        self.prorules = []
+        self.postprocessing = []
+
+        self.nr_sp_release = ""
+        self.nr_sp_seqs = ""
+        self.nr_total = (None, None)
+        self.nr_positive = (None, None)
+        self.nr_unknown = (None, None)
+        self.nr_false_pos = (None, None)
+        self.nr_false_neg = None
+        self.nr_partial = None
+
+        self.cc_taxo_range = ""
+        self.cc_max_repeat = ""
+        self.cc_site = []
+        self.cc_skip_flag = ""
+
+        self.dr_positive = []
+        self.dr_false_neg = []
+        self.dr_false_pos = []
+        self.dr_potential = []
+        self.dr_unknown = []
+
+        self.pdb_structs = []
+
+
+# Everything below are private functions
+
+
+def __read(handle):
+    import re
+
+    record = None
+    for line in handle:
+        keyword, value = line[:2], line[5:].rstrip()
+        if keyword == "ID":
+            record = Record()
+            cols = value.split("; ")
+            if len(cols) != 2:
+                raise ValueError(f"I don't understand identification line\n{line}")
+            record.name = cols[0]
+            record.type = cols[1].rstrip(".")  # don't want '.'
+        elif keyword == "AC":
+            record.accession = value.rstrip(";")
+        elif keyword == "DT":
+            # e.g. from January 2017,
+            # DT   01-APR-1990 CREATED; 01-APR-1990 DATA UPDATE; 01-APR-1990 INFO UPDATE.
+            # Older files had brackets round the date descriptions and used MMM-YYYY
+            dates = value.rstrip(".").split("; ")
+            if dates[0].endswith((" (CREATED)", " CREATED")):
+                # Remove last word
+                record.created = dates[0].rsplit(" ", 1)[0]
+            else:
+                raise ValueError(f"I don't understand date line\n{line}")
+            if dates[1].endswith((" (DATA UPDATE)", " DATA UPDATE")):
+                # Remove last two words
+                record.data_update = dates[1].rsplit(" ", 2)[0]
+            else:
+                raise ValueError(f"I don't understand date line\n{line}")
+            if dates[2].endswith((" (INFO UPDATE)", " INFO UPDATE")):
+                # Remove last two words
+                record.info_update = dates[2].rsplit(" ", 2)[0]
+            else:
+                raise ValueError(f"I don't understand date line\n{line}")
+        elif keyword == "DE":
+            record.description = value
+        elif keyword == "PA":
+            record.pattern += value
+        elif keyword == "MA":
+            record.matrix.append(value)
+        elif keyword == "PP":
+            record.postprocessing.extend(value.split(";"))
+        elif keyword == "RU":
+            record.rules.append(value)
+        elif keyword == "NR":
+            cols = value.split(";")
+            for col in cols:
+                if not col:
+                    continue
+                qual, data = (word.lstrip() for word in col.split("="))
+                if qual == "/RELEASE":
+                    release, seqs = data.split(",")
+                    record.nr_sp_release = release
+                    record.nr_sp_seqs = int(seqs)
+                elif qual == "/FALSE_NEG":
+                    record.nr_false_neg = int(data)
+                elif qual == "/PARTIAL":
+                    record.nr_partial = int(data)
+                elif qual in ["/TOTAL", "/POSITIVE", "/UNKNOWN", "/FALSE_POS"]:
+                    m = re.match(r"(\d+)\((\d+)\)", data)
+                    if not m:
+                        raise Exception(f"Broken data {data} in comment line\n{line!r}")
+                    hits = tuple(map(int, m.groups()))
+                    if qual == "/TOTAL":
+                        record.nr_total = hits
+                    elif qual == "/POSITIVE":
+                        record.nr_positive = hits
+                    elif qual == "/UNKNOWN":
+                        record.nr_unknown = hits
+                    elif qual == "/FALSE_POS":
+                        record.nr_false_pos = hits
+                else:
+                    raise ValueError(f"Unknown qual {qual} in comment line\n{line!r}")
+        elif keyword == "CC":
+            # Expect CC lines like this:
+            # CC   /TAXO-RANGE=??EPV; /MAX-REPEAT=2;
+            # Can (normally) split on ";" and then on "="
+            cols = value.split(";")
+            for col in cols:
+                if not col or col[:17] == "Automatic scaling":
+                    # DNAJ_2 in Release 15 has a non-standard comment line:
+                    # CC   Automatic scaling using reversed database
+                    # Throw it away.  (Should I keep it?)
+                    continue
+                if col.count("=") == 0:
+                    # Missing qualifier!  Can we recover gracefully?
+                    # For example, from Bug 2403, in PS50293 have:
+                    # CC /AUTHOR=K_Hofmann; N_Hulo
+                    continue
+                qual, data = (word.lstrip() for word in col.split("="))
+                if qual == "/TAXO-RANGE":
+                    record.cc_taxo_range = data
+                elif qual == "/MAX-REPEAT":
+                    record.cc_max_repeat = data
+                elif qual == "/SITE":
+                    pos, desc = data.split(",")
+                    record.cc_site.append((int(pos), desc))
+                elif qual == "/SKIP-FLAG":
+                    record.cc_skip_flag = data
+                elif qual == "/MATRIX_TYPE":
+                    record.cc_matrix_type = data
+                elif qual == "/SCALING_DB":
+                    record.cc_scaling_db = data
+                elif qual == "/AUTHOR":
+                    record.cc_author = data
+                elif qual == "/FT_KEY":
+                    record.cc_ft_key = data
+                elif qual == "/FT_DESC":
+                    record.cc_ft_desc = data
+                elif qual == "/VERSION":
+                    record.cc_version = data
+                else:
+                    raise ValueError(f"Unknown qual {qual} in comment line\n{line!r}")
+        elif keyword == "DR":
+            refs = value.split(";")
+            for ref in refs:
+                if not ref:
+                    continue
+                acc, name, type = (word.strip() for word in ref.split(","))
+                if type == "T":
+                    record.dr_positive.append((acc, name))
+                elif type == "F":
+                    record.dr_false_pos.append((acc, name))
+                elif type == "N":
+                    record.dr_false_neg.append((acc, name))
+                elif type == "P":
+                    record.dr_potential.append((acc, name))
+                elif type == "?":
+                    record.dr_unknown.append((acc, name))
+                else:
+                    raise ValueError(f"I don't understand type flag {type}")
+        elif keyword == "3D":
+            cols = value.split()
+            for id in cols:
+                record.pdb_structs.append(id.rstrip(";"))
+        elif keyword == "PR":
+            rules = value.split(";")
+            record.prorules.extend(rules)
+        elif keyword == "DO":
+            record.pdoc = value.rstrip(";")
+        elif keyword == "//":
+            if not record:
+                # Then this was the copyright statement
+                continue
+            break
+        else:
+            raise ValueError(f"Unknown keyword {keyword} found")
+    else:
+        return
+    if not record:
+        raise ValueError("Unexpected end of stream.")
+    return record

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/ScanProsite.py

@@ -0,0 +1,151 @@
+# Copyright 2009 by Michiel de Hoon. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code for calling and parsing ScanProsite from ExPASy."""
+
+from urllib.parse import urlencode
+from urllib.request import urlopen
+from xml.sax import handler
+from xml.sax.expatreader import ExpatParser
+
+# October 28th 2020 it was recognised that between October 10th 2020 and October
+# 28th the main url of prosite changed from https://www.expasy.org to
+# https://prosite.expasy.org. Thus a change in the mirror was issued from
+# https://www.expasy.org to https://prosite.expasy.org.
+PROSITE_URL = "https://prosite.expasy.org"
+
+
+class Record(list):
+    """Represents search results returned by ScanProsite.
+
+    This record is a list containing the search results returned by
+    ScanProsite. The record also contains the data members n_match,
+    n_seq, capped, and warning.
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.n_match = None
+        self.n_seq = None
+        self.capped = None
+        self.warning = None
+
+
+def scan(seq="", mirror=PROSITE_URL, output="xml", **keywords):
+    """Execute a ScanProsite search.
+
+    Arguments:
+     - mirror:   The ScanProsite mirror to be used
+                 (default: PROSITE_URL).
+     - seq:      The query sequence, or UniProtKB (Swiss-Prot,
+                 TrEMBL) accession
+     - output:   Format of the search results
+                 (default: xml)
+
+    Further search parameters can be passed as keywords; see the
+    documentation for programmatic access to ScanProsite at
+    https://prosite.expasy.org/scanprosite/scanprosite_doc.html
+    for a description of such parameters.
+
+    This function returns a handle to the search results returned by
+    ScanProsite. Search results in the XML format can be parsed into a
+    Python object, by using the Bio.ExPASy.ScanProsite.read function.
+
+    """
+    if output != "xml":
+        raise NotImplementedError("Only output='xml' is supported currently.")
+    parameters = {"seq": seq, "output": output}
+    for key, value in keywords.items():
+        if value is not None:
+            parameters[key] = value
+    command = urlencode(parameters)
+    url = f"{mirror}/cgi-bin/prosite/scanprosite/PSScan.cgi?{command}"
+    handle = urlopen(url)
+    return handle
+
+
+def read(handle):
+    """Parse search results returned by ScanProsite into a Python object."""
+    content_handler = ContentHandler()
+    saxparser = Parser()
+    saxparser.setContentHandler(content_handler)
+    saxparser.parse(handle)
+    record = content_handler.record
+    return record
+
+
+# The classes below are considered private
+
+
+class Parser(ExpatParser):
+    """Process the result from a ScanProsite search (PRIVATE)."""
+
+    def __init__(self):
+        """Initialize the class."""
+        ExpatParser.__init__(self)
+        self.firsttime = True
+
+    def feed(self, data, isFinal=0):
+        """Raise an Error if plain text is received in the data.
+
+        This is to show the Error messages returned by ScanProsite.
+        """
+        # Error messages returned by the ScanProsite server are formatted as
+        # as plain text instead of an XML document. To catch such error
+        # messages, we override the feed method of the Expat parser.
+        # The error message is (hopefully) contained in the data that was just
+        # fed to the parser.
+        if self.firsttime:
+            if data[:22].decode("utf-8") != "<scanprosite_response>":
+                raise ValueError(data)
+        self.firsttime = False
+        return ExpatParser.feed(self, data, isFinal)
+
+
+class ContentHandler(handler.ContentHandler):
+    """Process and fill in the records, results of the search (PRIVATE)."""
+
+    integers = ("start", "stop")
+    strings = (
+        "sequence_ac",
+        "sequence_id",
+        "sequence_db",
+        "signature_ac",
+        "level",
+        "level_tag",
+    )
+
+    def __init__(self):
+        """Initialize the class."""
+        self.element = []
+
+    def startElement(self, name, attrs):
+        """Define the beginning of a record and stores the search record."""
+        self.element.append(name)
+        self.content = ""
+        if self.element == ["scanprosite_response", "matchset"]:
+            self.record = Record()
+            self.record.n_match = int(attrs["n_match"])
+            self.record.n_seq = int(attrs["n_seq"])
+        elif self.element == ["scanprosite_response", "matchset", "match"]:
+            match = {}
+            self.record.append(match)
+
+    def endElement(self, name):
+        """Define the end of the search record."""
+        assert name == self.element.pop()
+        if self.element == ["scanprosite_response", "matchset", "match"]:
+            match = self.record[-1]
+            if name in ContentHandler.integers:
+                match[name] = int(self.content)
+            elif name in ContentHandler.strings:
+                match[name] = self.content
+            else:
+                # Unknown type, treat it as a string
+                match[name] = self.content
+
+    def characters(self, content):
+        """Store the record content."""
+        self.content += content

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/__init__.py

@@ -0,0 +1,138 @@
+# Copyright 2000 by Jeffrey Chang.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code to access resources at ExPASy over the WWW.
+
+See https://www.expasy.org/
+
+
+Functions:
+ - get_prodoc_entry  Interface to the get-prodoc-entry CGI script.
+ - get_prosite_entry Interface to the get-prosite-entry CGI script.
+ - get_prosite_raw   Interface to the get-prosite-raw CGI script.
+ - get_sprot_raw     Interface to the get-sprot-raw CGI script.
+
+"""
+
+import io
+from urllib.error import HTTPError
+from urllib.request import urlopen
+
+
+def get_prodoc_entry(
+    id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry"
+):
+    """Get a text handle to a PRODOC entry at ExPASy in HTML format.
+
+    >>> from Bio import ExPASy
+    >>> import os
+    >>> with ExPASy.get_prodoc_entry('PDOC00001') as in_handle:
+    ...     html = in_handle.read()
+    ...
+    >>> with open("myprodocrecord.html", "w") as out_handle:
+    ...     length = out_handle.write(html)
+    ...
+    >>> os.remove("myprodocrecord.html")  # tidy up
+
+    For a non-existing key XXX, ExPASy returns an HTML-formatted page
+    containing this text: 'There is currently no PROSITE entry for'
+    """
+    return _open(f"{cgi}?{id}")
+
+
+def get_prosite_entry(
+    id, cgi="https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry"
+):
+    """Get a text handle to a PROSITE entry at ExPASy in HTML format.
+
+    >>> from Bio import ExPASy
+    >>> import os
+    >>> with ExPASy.get_prosite_entry('PS00001') as in_handle:
+    ...     html = in_handle.read()
+    ...
+    >>> with open("myprositerecord.html", "w") as out_handle:
+    ...     length = out_handle.write(html)
+    ...
+    >>> os.remove("myprositerecord.html")  # tidy up
+
+    For a non-existing key XXX, ExPASy returns an HTML-formatted page
+    containing this text: 'There is currently no PROSITE entry for'
+    """
+    return _open(f"{cgi}?{id}")
+
+
+def get_prosite_raw(id, cgi=None):
+    """Get a text handle to a raw PROSITE or PRODOC record at ExPASy.
+
+    The cgi argument is deprecated due to changes in the ExPASy
+    website.
+
+    >>> from Bio import ExPASy
+    >>> from Bio.ExPASy import Prosite
+    >>> with ExPASy.get_prosite_raw('PS00001') as handle:
+    ...     record = Prosite.read(handle)
+    ...
+    >>> print(record.accession)
+    PS00001
+
+    This function raises a ValueError if the identifier does not exist:
+
+    >>> handle = ExPASy.get_prosite_raw("DOES_NOT_EXIST")
+    Traceback (most recent call last):
+        ...
+    ValueError: Failed to find entry 'DOES_NOT_EXIST' on ExPASy
+
+    """
+    try:
+        handle = _open(f"https://prosite.expasy.org/{id}.txt")
+    except HTTPError as exception:
+        if exception.code == 404:
+            raise ValueError("Failed to find entry '%s' on ExPASy" % id) from None
+        else:
+            raise
+    # This has happened historically, redirected to main page:
+    if handle.url == "https://www.expasy.org/":
+        raise ValueError(f"Failed to find entry '{id}' on ExPASy") from None
+    return handle
+
+
+def get_sprot_raw(id):
+    """Get a text handle to a raw SwissProt entry at ExPASy.
+
+    For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
+    (as per the https://www.expasy.org/expasy_urls.html documentation).
+
+    >>> from Bio import ExPASy
+    >>> from Bio import SwissProt
+    >>> with ExPASy.get_sprot_raw("O23729") as handle:
+    ...     record = SwissProt.read(handle)
+    ...
+    >>> print(record.entry_name)
+    CHS3_BROFI
+
+    This function raises a ValueError if the identifier does not exist:
+
+    >>> ExPASy.get_sprot_raw("DOES_NOT_EXIST")
+    Traceback (most recent call last):
+        ...
+    ValueError: Failed to find SwissProt entry 'DOES_NOT_EXIST'
+
+    """
+    try:
+        handle = _open(f"http://www.uniprot.org/uniprot/{id}.txt")
+    except HTTPError as exception:
+        if exception.code in (400, 404):
+            raise ValueError(f"Failed to find SwissProt entry '{id}'") from None
+        else:
+            raise
+    return handle
+
+
+def _open(url):
+    """Open URL and convert to text assuming UTF-8 encoding (PRIVATE)."""
+    handle = urlopen(url)
+    text_handle = io.TextIOWrapper(handle, encoding="UTF-8")
+    text_handle.url = handle.url
+    return text_handle

.venv_haddock/lib/python3.12/site-packages/Bio/ExPASy/cellosaurus.py

@@ -0,0 +1,208 @@
+# Copyright 2016 by Stephen Marshall.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Parser for the cellosaurus.txt file from ExPASy.
+
+See https://web.expasy.org/cellosaurus/
+
+Tested with the release of Version 18 (July 2016).
+
+Functions:
+ - read       Reads a file containing one cell line entry
+ - parse      Reads a file containing multiple cell line entries
+
+Classes:
+ - Record     Holds cell line data.
+
+Examples
+--------
+This example downloads the Cellosaurus database and parses it. Note that
+urlopen returns a stream of bytes, while the parser expects a stream of plain
+string, so we use TextIOWrapper to convert bytes to string using the UTF-8
+encoding. This is not needed if you download the cellosaurus.txt file in
+advance and open it (see the comment below).
+
+    >>> from urllib.request import urlopen
+    >>> from io import TextIOWrapper
+    >>> from Bio.ExPASy import cellosaurus
+    >>> url = "ftp://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt"
+    >>> bytestream = urlopen(url)
+    >>> textstream = TextIOWrapper(bytestream, "UTF-8")
+    >>> # alternatively, use
+    >>> # textstream = open("cellosaurus.txt")
+    >>> # if you downloaded the cellosaurus.txt file in advance.
+    >>> records = cellosaurus.parse(textstream)
+    >>> for record in records:
+    ...     if 'Homo sapiens' in record['OX'][0]:
+    ...         print(record['ID'])  # doctest:+ELLIPSIS
+    ...
+    #15310-LN
+    #W7079
+    (L)PC6
+    0.5alpha
+    ...
+
+"""
+
+
+def parse(handle):
+    """Parse cell line records.
+
+    This function is for parsing cell line files containing multiple
+    records.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    while True:
+        record = __read(handle)
+        if not record:
+            break
+        yield record
+
+
+def read(handle):
+    """Read one cell line record.
+
+    This function is for parsing cell line files containing
+    exactly one record.
+
+    Arguments:
+     - handle   - handle to the file.
+
+    """
+    record = __read(handle)
+    # We should have reached the end of the record by now
+    remainder = handle.read()
+    if remainder:
+        raise ValueError("More than one cell line record found")
+    return record
+
+
+class Record(dict):
+    """Holds information from an ExPASy Cellosaurus record as a Python dictionary.
+
+    Each record contains the following keys:
+
+    =========  ==============================  =======================
+    Line code  Content                         Occurrence in an entry
+    =========  ==============================  =======================
+    ID         Identifier (cell line name)     Once; starts an entry
+    AC         Accession (CVCL_xxxx)           Once
+    AS         Secondary accession number(s)   Optional; once
+    SY         Synonyms                        Optional; once
+    DR         Cross-references                Optional; once or more
+    RX         References identifiers          Optional: once or more
+    WW         Web pages                       Optional; once or more
+    CC         Comments                        Optional; once or more
+    ST         STR profile data                Optional; twice or more
+    DI         Diseases                        Optional; once or more
+    OX         Species of origin               Once or more
+    HI         Hierarchy                       Optional; once or more
+    OI         Originate from same individual  Optional; once or more
+    SX         Sex of cell                     Optional; once
+    AG         Age of donor at sampling        Optional; once
+    CA         Category                        Once
+    DT         Date (entry history)            Once
+    //         Terminator                      Once; ends an entry
+    =========  ==============================  =======================
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        dict.__init__(self)
+        self["ID"] = ""
+        self["AC"] = ""
+        self["AS"] = ""
+        self["SY"] = ""
+        self["DR"] = []
+        self["RX"] = []
+        self["WW"] = []
+        self["CC"] = []
+        self["ST"] = []
+        self["DI"] = []
+        self["OX"] = []
+        self["HI"] = []
+        self["OI"] = []
+        self["SX"] = ""
+        self["AG"] = ""
+        self["CA"] = ""
+        self["DT"] = ""
+
+    def __repr__(self):
+        """Return the canonical string representation of the Record object."""
+        if self["ID"]:
+            if self["AC"]:
+                return f"{self.__class__.__name__} ({self['ID']}, {self['AC']})"
+            else:
+                return f"{self.__class__.__name__} ({self['ID']})"
+        else:
+            return f"{self.__class__.__name__} ( )"
+
+    def __str__(self):
+        """Return a readable string representation of the Record object."""
+        output = "ID: " + self["ID"]
+        output += " AC: " + self["AC"]
+        output += " AS: " + self["AS"]
+        output += " SY: " + self["SY"]
+        output += " DR: " + repr(self["DR"])
+        output += " RX: " + repr(self["RX"])
+        output += " WW: " + repr(self["WW"])
+        output += " CC: " + repr(self["CC"])
+        output += " ST: " + repr(self["ST"])
+        output += " DI: " + repr(self["DI"])
+        output += " OX: " + repr(self["OX"])
+        output += " HI: " + repr(self["HI"])
+        output += " OI: " + repr(self["OI"])
+        output += " SX: " + self["SX"]
+        output += " AG: " + self["AG"]
+        output += " CA: " + self["CA"]
+        output += " DT: " + self["DT"]
+        return output
+
+
+# Everything below is private
+
+
+def __read(handle):
+    record = None
+
+    for line in handle:
+        key, value = line[:2], line[5:].rstrip()
+        if key == "ID":
+            record = Record()
+            record["ID"] = value
+        elif key in ["AC", "AS", "SY", "SX", "AG", "CA", "DT"]:
+            record[key] += value
+        elif key in [
+            # just append to the fields defined as lists, not to strings
+            "RX",
+            "WW",
+            "CC",
+            "ST",
+            "DI",
+            "OX",
+            "HI",
+            "OI",
+        ]:
+            record[key].append(value)
+        elif key == "DR":
+            k, v = value.split(";")
+            record["DR"].append((k.strip(), v.strip()))
+        elif key == "//":
+            if record:
+                return record
+            else:
+                continue
+    if record:
+        raise ValueError("Unexpected end of stream")
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/File.py

@@ -0,0 +1,626 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# Copyright 2009-2018 by Peter Cock. All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Code for more fancy file handles.
+
+Bio.File defines private classes used in Bio.SeqIO and Bio.SearchIO for
+indexing files. These are not intended for direct use.
+"""
+
+import collections.abc
+import contextlib
+import itertools
+import os
+from abc import ABC
+from abc import abstractmethod
+
+try:
+    import sqlite3
+except ImportError:
+    # May be missing if Python was compiled from source without its dependencies
+    sqlite3 = None  # type: ignore
+
+
+@contextlib.contextmanager
+def as_handle(handleish, mode="r", **kwargs):
+    r"""Context manager to ensure we are using a handle.
+
+    Context manager for arguments that can be passed to SeqIO and AlignIO read, write,
+    and parse methods: either file objects or path-like objects (strings, pathlib.Path
+    instances, or more generally, anything that can be handled by the builtin 'open'
+    function).
+
+    When given a path-like object, returns an open file handle to that path, with provided
+    mode, which will be closed when the manager exits.
+
+    All other inputs are returned, and are *not* closed.
+
+    Arguments:
+     - handleish  - Either a file handle or path-like object (anything which can be
+                    passed to the builtin 'open' function, such as str, bytes,
+                    pathlib.Path, and os.DirEntry objects)
+     - mode       - Mode to open handleish (used only if handleish is a string)
+     - kwargs     - Further arguments to pass to open(...)
+
+    Examples
+    --------
+    >>> from Bio import File
+    >>> import os
+    >>> with File.as_handle('seqs.fasta', 'w') as fp:
+    ...     fp.write('>test\nACGT')
+    ...
+    10
+    >>> fp.closed
+    True
+
+    >>> handle = open('seqs.fasta', 'w')
+    >>> with File.as_handle(handle) as fp:
+    ...     fp.write('>test\nACGT')
+    ...
+    10
+    >>> fp.closed
+    False
+    >>> fp.close()
+    >>> os.remove("seqs.fasta")  # tidy up
+
+    """
+    try:
+        with open(handleish, mode, **kwargs) as fp:
+            yield fp
+    except TypeError:
+        yield handleish
+
+
+def _open_for_random_access(filename):
+    """Open a file in binary mode, spot if it is BGZF format etc (PRIVATE).
+
+    This functionality is used by the Bio.SeqIO and Bio.SearchIO index
+    and index_db functions.
+
+    If the file is gzipped but not BGZF, a specific ValueError is raised.
+    """
+    handle = open(filename, "rb")
+    magic = handle.read(2)
+    handle.seek(0)
+
+    if magic == b"\x1f\x8b":
+        # This is a gzipped file, but is it BGZF?
+        from . import bgzf
+
+        try:
+            # If it is BGZF, we support that
+            return bgzf.BgzfReader(mode="rb", fileobj=handle)
+        except ValueError as e:
+            assert "BGZF" in str(e)
+            # Not a BGZF file after all,
+            handle.close()
+            raise ValueError(
+                "Gzipped files are not suitable for indexing, "
+                "please use BGZF (blocked gzip format) instead."
+            ) from None
+
+    return handle
+
+
+# The rest of this file defines code used in Bio.SeqIO and Bio.SearchIO
+# for indexing
+
+
+class _IndexedSeqFileProxy(ABC):
+    """Abstract base class for file format specific random access (PRIVATE).
+
+    This is subclasses in both Bio.SeqIO for indexing as SeqRecord
+    objects, and in Bio.SearchIO for indexing QueryResult objects.
+
+    Subclasses for each file format should define '__iter__', 'get'
+    and optionally 'get_raw' methods.
+    """
+
+    @abstractmethod
+    def __iter__(self):
+        """Return (identifier, offset, length in bytes) tuples.
+
+        The length can be zero where it is not implemented or not
+        possible for a particular file format.
+        """
+        raise NotImplementedError
+
+    @abstractmethod
+    def get(self, offset):
+        """Return parsed object for this entry."""
+        # Most file formats with self contained records can be handled by
+        # parsing StringIO(self.get_raw(offset).decode())
+        raise NotImplementedError
+
+    def get_raw(self, offset):
+        """Return the raw record from the file as a bytes string (if implemented).
+
+        If the key is not found, a KeyError exception is raised.
+
+        This may not have been implemented for all file formats.
+        """
+        # Should be done by each sub-class (if possible)
+        raise NotImplementedError("Not available for this file format.")
+
+
+class _IndexedSeqFileDict(collections.abc.Mapping):
+    """Read only dictionary interface to a sequential record file.
+
+    This code is used in both Bio.SeqIO for indexing as SeqRecord
+    objects, and in Bio.SearchIO for indexing QueryResult objects.
+
+    Keeps the keys and associated file offsets in memory, reads the file
+    to access entries as objects parsing them on demand. This approach
+    is memory limited, but will work even with millions of records.
+
+    Note duplicate keys are not allowed. If this happens, a ValueError
+    exception is raised.
+
+    As used in Bio.SeqIO, by default the SeqRecord's id string is used
+    as the dictionary key. In Bio.SearchIO, the query's id string is
+    used. This can be changed by supplying an optional key_function,
+    a callback function which will be given the record id and must
+    return the desired key. For example, this allows you to parse
+    NCBI style FASTA identifiers, and extract the GI number to use
+    as the dictionary key.
+
+    Note that this dictionary is essentially read only. You cannot
+    add or change values, pop values, nor clear the dictionary.
+    """
+
+    def __init__(self, random_access_proxy, key_function, repr, obj_repr):
+        """Initialize the class."""
+        # Use key_function=None for default value
+        self._proxy = random_access_proxy
+        self._key_function = key_function
+        self._repr = repr
+        self._obj_repr = obj_repr
+        self._cached_prev_record = (None, None)  # (key, record)
+        if key_function:
+            offset_iter = (
+                (key_function(key), offset, length)
+                for (key, offset, length) in random_access_proxy
+            )
+        else:
+            offset_iter = random_access_proxy
+        offsets = {}
+        for key, offset, length in offset_iter:
+            # Note - we don't store the length because I want to minimise the
+            # memory requirements. With the SQLite backend the length is kept
+            # and is used to speed up the get_raw method (by about 3 times).
+            # The length should be provided by all the current backends except
+            # SFF where there is an existing Roche index we can reuse (very fast
+            # but lacks the record lengths)
+            # assert length or format in ["sff", "sff-trim"], \
+            #       "%s at offset %i given length %r (%s format %s)" \
+            #       % (key, offset, length, filename, format)
+            if key in offsets:
+                self._proxy._handle.close()
+                raise ValueError(f"Duplicate key '{key}'")
+            else:
+                offsets[key] = offset
+        self._offsets = offsets
+
+    def __repr__(self):
+        """Return a string representation of the File object."""
+        return self._repr
+
+    def __str__(self):
+        """Create a string representation of the File object."""
+        # TODO - How best to handle the __str__ for SeqIO and SearchIO?
+        if self:
+            return f"{{{list(self.keys())[0]!r} : {self._obj_repr}(...), ...}}"
+        else:
+            return "{}"
+
+    def __len__(self):
+        """Return the number of records."""
+        return len(self._offsets)
+
+    def __iter__(self):
+        """Iterate over the keys."""
+        return iter(self._offsets)
+
+    def __getitem__(self, key):
+        """Return record for the specified key.
+
+        As an optimization when repeatedly asked to look up the same record,
+        the key and record are cached so that if the *same* record is
+        requested next time, it can be returned without going to disk.
+        """
+        if key == self._cached_prev_record[0]:
+            return self._cached_prev_record[1]
+        # Pass the offset to the proxy
+        record = self._proxy.get(self._offsets[key])
+        if self._key_function:
+            key2 = self._key_function(record.id)
+        else:
+            key2 = record.id
+        if key != key2:
+            raise ValueError(f"Key did not match ({key} vs {key2})")
+        self._cached_prev_record = (key, record)
+        return record
+
+    def get_raw(self, key):
+        """Return the raw record from the file as a bytes string.
+
+        If the key is not found, a KeyError exception is raised.
+        """
+        # Pass the offset to the proxy
+        return self._proxy.get_raw(self._offsets[key])
+
+    def close(self):
+        """Close the file handle being used to read the data.
+
+        Once called, further use of the index won't work. The sole purpose
+        of this method is to allow explicit handle closure - for example
+        if you wish to delete the file, on Windows you must first close
+        all open handles to that file.
+        """
+        self._proxy._handle.close()
+
+
+class _SQLiteManySeqFilesDict(_IndexedSeqFileDict):
+    """Read only dictionary interface to many sequential record files.
+
+    This code is used in both Bio.SeqIO for indexing as SeqRecord
+    objects, and in Bio.SearchIO for indexing QueryResult objects.
+
+    Keeps the keys, file-numbers and offsets in an SQLite database. To access
+    a record by key, reads from the offset in the appropriate file and then
+    parses the record into an object.
+
+    There are OS limits on the number of files that can be open at once,
+    so a pool are kept. If a record is required from a closed file, then
+    one of the open handles is closed first.
+    """
+
+    def __init__(
+        self,
+        index_filename,
+        filenames,
+        proxy_factory,
+        fmt,
+        key_function,
+        repr,
+        max_open=10,
+    ):
+        """Initialize the class."""
+        # TODO? - Don't keep filename list in memory (just in DB)?
+        # Should save a chunk of memory if dealing with 1000s of files.
+        # Furthermore could compare a generator to the DB on reloading
+        # (no need to turn it into a list)
+
+        if sqlite3 is None:
+            # Python was compiled without sqlite3 support
+            from Bio import MissingPythonDependencyError
+
+            raise MissingPythonDependencyError(
+                "Python was compiled without the sqlite3 module"
+            )
+        if filenames is not None:
+            filenames = list(filenames)  # In case it was a generator
+
+        # Cache the arguments as private variables
+        self._index_filename = index_filename
+        self._filenames = filenames
+        self._format = fmt
+        self._key_function = key_function
+        self._proxy_factory = proxy_factory
+        self._repr = repr
+        self._max_open = max_open
+        self._proxies = {}
+
+        # Note if using SQLite :memory: trick index filename, this will
+        # give $PWD as the relative path (which is fine).
+        self._relative_path = os.path.abspath(os.path.dirname(index_filename))
+
+        if os.path.isfile(index_filename):
+            self._load_index()
+        else:
+            self._build_index()
+
+    def _load_index(self):
+        """Call from __init__ to reuse an existing index (PRIVATE)."""
+        index_filename = self._index_filename
+        relative_path = self._relative_path
+        filenames = self._filenames
+        fmt = self._format
+        proxy_factory = self._proxy_factory
+
+        con = sqlite3.dbapi2.connect(index_filename, check_same_thread=False)
+        self._con = con
+        # Check the count...
+        try:
+            (count,) = con.execute(
+                "SELECT value FROM meta_data WHERE key=?;", ("count",)
+            ).fetchone()
+            self._length = int(count)
+            if self._length == -1:
+                con.close()
+                raise ValueError("Unfinished/partial database") from None
+
+            # use MAX(_ROWID_) to obtain the number of sequences in the database
+            # using COUNT(key) is quite slow in SQLITE
+            # (https://stackoverflow.com/questions/8988915/sqlite-count-slow-on-big-tables)
+            (count,) = con.execute("SELECT MAX(_ROWID_) FROM offset_data;").fetchone()
+            if self._length != int(count):
+                con.close()
+                raise ValueError(
+                    "Corrupt database? %i entries not %i" % (int(count), self._length)
+                ) from None
+            (self._format,) = con.execute(
+                "SELECT value FROM meta_data WHERE key=?;", ("format",)
+            ).fetchone()
+            if fmt and fmt != self._format:
+                con.close()
+                raise ValueError(
+                    f"Index file says format {self._format}, not {fmt}"
+                ) from None
+            try:
+                (filenames_relative_to_index,) = con.execute(
+                    "SELECT value FROM meta_data WHERE key=?;",
+                    ("filenames_relative_to_index",),
+                ).fetchone()
+                filenames_relative_to_index = (
+                    filenames_relative_to_index.upper() == "TRUE"
+                )
+            except TypeError:
+                # Original behaviour, assume if meta_data missing
+                filenames_relative_to_index = False
+            self._filenames = [
+                row[0]
+                for row in con.execute(
+                    "SELECT name FROM file_data ORDER BY file_number;"
+                ).fetchall()
+            ]
+            if filenames_relative_to_index:
+                # Not implicitly relative to $PWD, explicitly relative to index file
+                relative_path = os.path.abspath(os.path.dirname(index_filename))
+                tmp = []
+                for f in self._filenames:
+                    if os.path.isabs(f):
+                        tmp.append(f)
+                    else:
+                        # Would be stored with Unix / path separator, so convert
+                        # it to the local OS path separator here:
+                        tmp.append(
+                            os.path.join(relative_path, f.replace("/", os.path.sep))
+                        )
+                self._filenames = tmp
+                del tmp
+            if filenames and len(filenames) != len(self._filenames):
+                con.close()
+                raise ValueError(
+                    "Index file says %i files, not %i"
+                    % (len(self._filenames), len(filenames))
+                ) from None
+            if filenames and filenames != self._filenames:
+                for old, new in zip(self._filenames, filenames):
+                    # Want exact match (after making relative to the index above)
+                    if os.path.abspath(old) != os.path.abspath(new):
+                        con.close()
+                        if filenames_relative_to_index:
+                            raise ValueError(
+                                "Index file has different filenames, e.g. %r != %r"
+                                % (os.path.abspath(old), os.path.abspath(new))
+                            ) from None
+                        else:
+                            raise ValueError(
+                                "Index file has different filenames "
+                                "[This is an old index where any relative paths "
+                                "were relative to the original working directory]. "
+                                "e.g. %r != %r"
+                                % (os.path.abspath(old), os.path.abspath(new))
+                            ) from None
+                # Filenames are equal (after imposing abspath)
+        except sqlite3.OperationalError as err:
+            con.close()
+            raise ValueError(f"Not a Biopython index database? {err}") from None
+        # Now we have the format (from the DB if not given to us),
+        if not proxy_factory(self._format):
+            con.close()
+            raise ValueError(f"Unsupported format '{self._format}'")
+
+    def _build_index(self):
+        """Call from __init__ to create a new index (PRIVATE)."""
+        index_filename = self._index_filename
+        relative_path = self._relative_path
+        filenames = self._filenames
+        fmt = self._format
+        key_function = self._key_function
+        proxy_factory = self._proxy_factory
+        max_open = self._max_open
+        random_access_proxies = self._proxies
+
+        if not fmt or not filenames:
+            raise ValueError(
+                f"Filenames to index and format required to build {index_filename!r}"
+            )
+        if not proxy_factory(fmt):
+            raise ValueError(f"Unsupported format '{fmt}'")
+        # Create the index
+        con = sqlite3.dbapi2.connect(index_filename)
+        self._con = con
+        # print("Creating index")
+        # Sqlite PRAGMA settings for speed
+        con.execute("PRAGMA synchronous=OFF")
+        con.execute("PRAGMA locking_mode=EXCLUSIVE")
+        # Don't index the key column until the end (faster)
+        # con.execute("CREATE TABLE offset_data (key TEXT PRIMARY KEY, "
+        #             "offset INTEGER);")
+        con.execute("CREATE TABLE meta_data (key TEXT, value TEXT);")
+        con.execute("INSERT INTO meta_data (key, value) VALUES (?,?);", ("count", -1))
+        con.execute("INSERT INTO meta_data (key, value) VALUES (?,?);", ("format", fmt))
+        con.execute(
+            "INSERT INTO meta_data (key, value) VALUES (?,?);",
+            ("filenames_relative_to_index", "True"),
+        )
+        # TODO - Record the file size and modified date?
+        con.execute("CREATE TABLE file_data (file_number INTEGER, name TEXT);")
+        con.execute(
+            "CREATE TABLE offset_data (key TEXT, "
+            "file_number INTEGER, offset INTEGER, length INTEGER);"
+        )
+        count = 0
+        for file_index, filename in enumerate(filenames):
+            # Default to storing as an absolute path,
+            f = os.path.abspath(filename)
+            if not os.path.isabs(filename) and not os.path.isabs(index_filename):
+                # Since user gave BOTH filename & index as relative paths,
+                # we will store this relative to the index file even though
+                # if it may now start ../ (meaning up a level)
+                # Note for cross platform use (e.g. shared drive over SAMBA),
+                # convert any Windows slash into Unix style for rel paths.
+                f = os.path.relpath(filename, relative_path).replace(os.path.sep, "/")
+            elif (os.path.dirname(os.path.abspath(filename)) + os.path.sep).startswith(
+                relative_path + os.path.sep
+            ):
+                # Since sequence file is in same directory or sub directory,
+                # might as well make this into a relative path:
+                f = os.path.relpath(filename, relative_path).replace(os.path.sep, "/")
+                assert not f.startswith("../"), f
+            # print("DEBUG - storing %r as [%r] %r" % (filename, relative_path, f))
+            con.execute(
+                "INSERT INTO file_data (file_number, name) VALUES (?,?);",
+                (file_index, f),
+            )
+            random_access_proxy = proxy_factory(fmt, filename)
+            if key_function:
+                offset_iter = (
+                    (key_function(key), file_index, offset, length)
+                    for (key, offset, length) in random_access_proxy
+                )
+            else:
+                offset_iter = (
+                    (key, file_index, offset, length)
+                    for (key, offset, length) in random_access_proxy
+                )
+            while True:
+                batch = list(itertools.islice(offset_iter, 100))
+                if not batch:
+                    break
+                # print("Inserting batch of %i offsets, %s ... %s"
+                #       % (len(batch), batch[0][0], batch[-1][0]))
+                con.executemany(
+                    "INSERT INTO offset_data (key,file_number,offset,length) VALUES (?,?,?,?);",
+                    batch,
+                )
+                con.commit()
+                count += len(batch)
+            if len(random_access_proxies) < max_open:
+                random_access_proxies[file_index] = random_access_proxy
+            else:
+                random_access_proxy._handle.close()
+        self._length = count
+        # print("About to index %i entries" % count)
+        try:
+            con.execute(
+                "CREATE UNIQUE INDEX IF NOT EXISTS key_index ON offset_data(key);"
+            )
+        except sqlite3.IntegrityError as err:
+            self._proxies = random_access_proxies
+            self.close()
+            con.close()
+            raise ValueError(f"Duplicate key? {err}") from None
+        con.execute("PRAGMA locking_mode=NORMAL")
+        con.execute("UPDATE meta_data SET value = ? WHERE key = ?;", (count, "count"))
+        con.commit()
+        # print("Index created")
+
+    def __repr__(self):
+        return self._repr
+
+    def __contains__(self, key):
+        return bool(
+            self._con.execute(
+                "SELECT key FROM offset_data WHERE key=?;", (key,)
+            ).fetchone()
+        )
+
+    def __len__(self):
+        """Return the number of records indexed."""
+        return self._length
+        # return self._con.execute("SELECT COUNT(key) FROM offset_data;").fetchone()[0]
+
+    def __iter__(self):
+        """Iterate over the keys."""
+        for row in self._con.execute(
+            "SELECT key FROM offset_data ORDER BY file_number, offset;"
+        ):
+            yield str(row[0])
+
+    def __getitem__(self, key):
+        """Return record for the specified key."""
+        # Pass the offset to the proxy
+        row = self._con.execute(
+            "SELECT file_number, offset FROM offset_data WHERE key=?;", (key,)
+        ).fetchone()
+        if not row:
+            raise KeyError
+        file_number, offset = row
+        proxies = self._proxies
+        if file_number in proxies:
+            record = proxies[file_number].get(offset)
+        else:
+            if len(proxies) >= self._max_open:
+                # Close an old handle...
+                proxies.popitem()[1]._handle.close()
+            # Open a new handle...
+            proxy = self._proxy_factory(self._format, self._filenames[file_number])
+            record = proxy.get(offset)
+            proxies[file_number] = proxy
+        if self._key_function:
+            key2 = self._key_function(record.id)
+        else:
+            key2 = record.id
+        if key != key2:
+            raise ValueError(f"Key did not match ({key} vs {key2})")
+        return record
+
+    def get_raw(self, key):
+        """Return the raw record from the file as a bytes string.
+
+        If the key is not found, a KeyError exception is raised.
+        """
+        # Pass the offset to the proxy
+        row = self._con.execute(
+            "SELECT file_number, offset, length FROM offset_data WHERE key=?;", (key,)
+        ).fetchone()
+        if not row:
+            raise KeyError
+        file_number, offset, length = row
+        proxies = self._proxies
+        if file_number in proxies:
+            if length:
+                # Shortcut if we have the length
+                h = proxies[file_number]._handle
+                h.seek(offset)
+                return h.read(length)
+            else:
+                return proxies[file_number].get_raw(offset)
+        else:
+            # This code is duplicated from __getitem__ to avoid a function call
+            if len(proxies) >= self._max_open:
+                # Close an old handle...
+                proxies.popitem()[1]._handle.close()
+            # Open a new handle...
+            proxy = self._proxy_factory(self._format, self._filenames[file_number])
+            proxies[file_number] = proxy
+            if length:
+                # Shortcut if we have the length
+                h = proxy._handle
+                h.seek(offset)
+                return h.read(length)
+            else:
+                return proxy.get_raw(offset)
+
+    def close(self):
+        """Close any open file handles."""
+        proxies = self._proxies
+        while proxies:
+            proxies.popitem()[1]._handle.close()

.venv_haddock/lib/python3.12/site-packages/Bio/GenBank/Record.py

@@ -0,0 +1,669 @@
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+#
+
+"""Hold GenBank data in a straightforward format.
+
+Classes:
+ - Record - All of the information in a GenBank record.
+ - Reference - hold reference data for a record.
+ - Feature - Hold the information in a Feature Table.
+ - Qualifier - Qualifiers on a Feature.
+
+"""
+
+import Bio.GenBank
+
+
+def _wrapped_genbank(information, indent, wrap_space=1, split_char=" "):
+    """Write a line of GenBank info that can wrap over multiple lines (PRIVATE).
+
+    This takes a line of information which can potentially wrap over
+    multiple lines, and breaks it up with carriage returns and
+    indentation so it fits properly into a GenBank record.
+
+    Arguments:
+     - information - The string holding the information we want
+       wrapped in GenBank method.
+     - indent - The indentation on the lines we are writing.
+     - wrap_space - Whether or not to wrap only on spaces in the
+       information.
+     - split_char - A specific character to split the lines on. By default
+       spaces are used.
+
+    """
+    info_length = Record.GB_LINE_LENGTH - indent
+
+    if not information:
+        # GenBank files use "." for missing data
+        return ".\n"
+
+    if wrap_space:
+        info_parts = information.split(split_char)
+    else:
+        cur_pos = 0
+        info_parts = []
+        while cur_pos < len(information):
+            info_parts.append(information[cur_pos : cur_pos + info_length])
+            cur_pos += info_length
+
+    # first get the information string split up by line
+    output_parts = []
+    cur_part = ""
+    for info_part in info_parts:
+        if len(cur_part) + 1 + len(info_part) > info_length:
+            if cur_part:
+                if split_char != " ":
+                    cur_part += split_char
+                output_parts.append(cur_part)
+            cur_part = info_part
+        else:
+            if cur_part == "":
+                cur_part = info_part
+            else:
+                cur_part += split_char + info_part
+
+    # add the last bit of information to the output
+    if cur_part:
+        output_parts.append(cur_part)
+
+    # now format the information string for return
+    output_info = output_parts[0] + "\n"
+    for output_part in output_parts[1:]:
+        output_info += " " * indent + output_part + "\n"
+
+    return output_info
+
+
+def _indent_genbank(information, indent):
+    """Write out information with the specified indent (PRIVATE).
+
+    Unlike _wrapped_genbank, this function makes no attempt to wrap
+    lines -- it assumes that the information already has newlines in the
+    appropriate places, and will add the specified indent to the start of
+    each line.
+    """
+    # split the info into lines based on line breaks
+    info_parts = information.split("\n")
+
+    # the first line will have no indent
+    output_info = info_parts[0] + "\n"
+    for info_part in info_parts[1:]:
+        output_info += " " * indent + info_part + "\n"
+
+    return output_info
+
+
+class Record:
+    """Hold GenBank information in a format similar to the original record.
+
+    The Record class is meant to make data easy to get to when you are
+    just interested in looking at GenBank data.
+
+    Attributes:
+     - locus - The name specified after the LOCUS keyword in the GenBank
+       record. This may be the accession number, or a clone id or something else.
+     - size - The size of the record.
+     - residue_type - The type of residues making up the sequence in this
+       record. Normally something like RNA, DNA or PROTEIN, but may be as
+       esoteric as 'ss-RNA circular'.
+     - data_file_division - The division this record is stored under in
+       GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT -> bacteria...)
+     - date - The date of submission of the record, in a form like '28-JUL-1998'
+     - accession - list of all accession numbers for the sequence.
+     - nid - Nucleotide identifier number.
+     - pid - Proteint identifier number
+     - version - The accession number + version (ie. AB01234.2)
+     - db_source - Information about the database the record came from
+     - gi - The NCBI gi identifier for the record.
+     - keywords - A list of keywords related to the record.
+     - segment - If the record is one of a series, this is info about which
+       segment this record is (something like '1 of 6').
+     - source - The source of material where the sequence came from.
+     - organism - The genus and species of the organism (ie. 'Homo sapiens')
+     - taxonomy - A listing of the taxonomic classification of the organism,
+       starting general and getting more specific.
+     - references - A list of Reference objects.
+     - comment - Text with any kind of comment about the record.
+     - features - A listing of Features making up the feature table.
+     - base_counts - A string with the counts of bases for the sequence.
+     - origin - A string specifying info about the origin of the sequence.
+     - sequence - A string with the sequence itself.
+     - contig - A string of location information for a CONTIG in a RefSeq file
+     - project - The genome sequencing project numbers
+       (will be replaced by the dblink cross-references in 2009).
+     - dblinks - The genome sequencing project number(s) and other links.
+       (will replace the project information in 2009).
+
+    """
+
+    # constants for outputting GenBank information
+    GB_LINE_LENGTH = 79
+    GB_BASE_INDENT = 12
+    GB_FEATURE_INDENT = 21
+    GB_INTERNAL_INDENT = 2
+    GB_OTHER_INTERNAL_INDENT = 3
+    GB_FEATURE_INTERNAL_INDENT = 5
+    GB_SEQUENCE_INDENT = 9
+
+    BASE_FORMAT = "%-" + str(GB_BASE_INDENT) + "s"
+    INTERNAL_FORMAT = (
+        " " * GB_INTERNAL_INDENT + "%-" + str(GB_BASE_INDENT - GB_INTERNAL_INDENT) + "s"
+    )
+    OTHER_INTERNAL_FORMAT = (
+        " " * GB_OTHER_INTERNAL_INDENT
+        + "%-"
+        + str(GB_BASE_INDENT - GB_OTHER_INTERNAL_INDENT)
+        + "s"
+    )
+
+    BASE_FEATURE_FORMAT = "%-" + str(GB_FEATURE_INDENT) + "s"
+    INTERNAL_FEATURE_FORMAT = (
+        " " * GB_FEATURE_INTERNAL_INDENT
+        + "%-"
+        + str(GB_FEATURE_INDENT - GB_FEATURE_INTERNAL_INDENT)
+        + "s"
+    )
+    SEQUENCE_FORMAT = "%" + str(GB_SEQUENCE_INDENT) + "s"
+
+    def __init__(self):
+        """Initialize the class."""
+        self.accession = []
+        self.base_counts = ""
+        self.comment = ""
+        self.contig = ""
+        self.data_file_division = ""
+        self.date = ""
+        self.db_source = ""
+        self.dblinks = []
+        self.definition = ""
+        self.features = []
+        self.gi = ""
+        self.keywords = []
+        self.locus = ""
+        self.molecule_type = ""
+        self.nid = ""
+        self.organism = ""
+        self.origin = ""
+        self.pid = ""
+        self.primary = []
+        self.projects = []
+        self.references = []
+        self.residue_type = ""
+        self.segment = ""
+        self.sequence = ""
+        self.size = ""
+        self.source = ""
+        self.taxonomy = []
+        self.topology = ""
+        self.version = ""
+        self.wgs = ""
+        self.wgs_scafld = []
+
+    def __str__(self):
+        """Provide a GenBank formatted output option for a Record.
+
+        The objective of this is to provide an easy way to read in a GenBank
+        record, modify it somehow, and then output it in 'GenBank format.'
+        We are striving to make this work so that a parsed Record that is
+        output using this function will look exactly like the original
+        record.
+
+        Much of the output is based on format description info at:
+
+        ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt
+        """
+        output = self._locus_line()
+        output += self._definition_line()
+        output += self._accession_line()
+        output += self._version_line()
+        output += self._project_line()
+        output += self._dblink_line()
+        output += self._nid_line()
+        output += self._pid_line()
+        output += self._keywords_line()
+        output += self._db_source_line()
+        output += self._segment_line()
+        output += self._source_line()
+        output += self._organism_line()
+        for reference in self.references:
+            output += str(reference)
+        output += self._comment_line()
+        output += self._features_line()
+        for feature in self.features:
+            output += str(feature)
+        output += self._base_count_line()
+        output += self._origin_line()
+        output += self._sequence_line()
+        output += self._wgs_line()
+        output += self._wgs_scafld_line()
+        output += self._contig_line()
+        output += "//"
+        return output
+
+    def _locus_line(self):
+        """Provide the output string for the LOCUS line (PRIVATE)."""
+        output = "LOCUS"
+        output += " " * 7  # 6-12 spaces
+        output += "%-9s" % self.locus
+        output += " "  # 22 space
+        output += "%7s" % self.size
+        if "PROTEIN" in self.residue_type:
+            output += " aa"
+        else:
+            output += " bp "
+
+        # treat circular types differently, since they'll have long residue
+        # types
+        if "circular" in self.residue_type:
+            output += "%17s" % self.residue_type
+        # second case: ss-DNA types of records
+        elif "-" in self.residue_type:
+            output += "%7s" % self.residue_type
+            output += " " * 10  # spaces for circular
+        else:
+            output += " " * 3  # spaces for stuff like ss-
+            output += "%-4s" % self.residue_type
+            output += " " * 10  # spaces for circular
+
+        output += " " * 2
+        output += "%3s" % self.data_file_division
+        output += " " * 7  # spaces for 56-63
+        output += "%11s" % self.date
+        output += "\n"
+        return output
+
+    def _definition_line(self):
+        """Provide output for the DEFINITION line (PRIVATE)."""
+        output = Record.BASE_FORMAT % "DEFINITION"
+        output += _wrapped_genbank(self.definition + ".", Record.GB_BASE_INDENT)
+        return output
+
+    def _accession_line(self):
+        """Output for the ACCESSION line (PRIVATE)."""
+        if self.accession:
+            output = Record.BASE_FORMAT % "ACCESSION"
+
+            acc_info = ""
+            for accession in self.accession:
+                acc_info += f"{accession} "
+            # strip off an extra space at the end
+            acc_info = acc_info.rstrip()
+            output += _wrapped_genbank(acc_info, Record.GB_BASE_INDENT)
+        else:
+            output = ""
+
+        return output
+
+    def _version_line(self):
+        """Output for the VERSION line (PRIVATE)."""
+        if self.version:
+            output = Record.BASE_FORMAT % "VERSION"
+            output += self.version
+            output += "  GI:"
+            output += f"{self.gi}\n"
+        else:
+            output = ""
+        return output
+
+    def _project_line(self):
+        output = ""
+        if len(self.projects) > 0:
+            output = Record.BASE_FORMAT % "PROJECT"
+            output += f"{'  '.join(self.projects)}\n"
+        return output
+
+    def _dblink_line(self):
+        output = ""
+        if len(self.dblinks) > 0:
+            output = Record.BASE_FORMAT % "DBLINK"
+            dblink_info = "\n".join(self.dblinks)
+            output += _wrapped_genbank(dblink_info, Record.GB_BASE_INDENT)
+        return output
+
+    def _nid_line(self):
+        """Output for the NID line. Use of NID is obsolete in GenBank files (PRIVATE)."""
+        if self.nid:
+            output = Record.BASE_FORMAT % "NID"
+            output += f"{self.nid}\n"
+        else:
+            output = ""
+        return output
+
+    def _pid_line(self):
+        """Output for PID line. Presumedly, PID usage is also obsolete (PRIVATE)."""
+        if self.pid:
+            output = Record.BASE_FORMAT % "PID"
+            output += f"{self.pid}\n"
+        else:
+            output = ""
+        return output
+
+    def _keywords_line(self):
+        """Output for the KEYWORDS line (PRIVATE)."""
+        output = ""
+        if self.keywords:
+            output += Record.BASE_FORMAT % "KEYWORDS"
+            keyword_info = ""
+            for keyword in self.keywords:
+                keyword_info += f"{keyword}; "
+            # replace the ; at the end with a period
+            keyword_info = keyword_info[:-2]
+            keyword_info += "."
+
+            output += _wrapped_genbank(keyword_info, Record.GB_BASE_INDENT)
+
+        return output
+
+    def _db_source_line(self):
+        """Output for DBSOURCE line (PRIVATE)."""
+        if self.db_source:
+            output = Record.BASE_FORMAT % "DBSOURCE"
+            output += f"{self.db_source}\n"
+        else:
+            output = ""
+        return output
+
+    def _segment_line(self):
+        """Output for the SEGMENT line (PRIVATE)."""
+        output = ""
+        if self.segment:
+            output += Record.BASE_FORMAT % "SEGMENT"
+            output += _wrapped_genbank(self.segment, Record.GB_BASE_INDENT)
+        return output
+
+    def _source_line(self):
+        """Output for SOURCE line on where the sample came from (PRIVATE)."""
+        output = Record.BASE_FORMAT % "SOURCE"
+        output += _wrapped_genbank(self.source, Record.GB_BASE_INDENT)
+        return output
+
+    def _organism_line(self):
+        """Output for ORGANISM line with taxonomy info (PRIVATE)."""
+        output = Record.INTERNAL_FORMAT % "ORGANISM"
+        # Now that species names can be too long, this line can wrap (Bug 2591)
+        output += _wrapped_genbank(self.organism, Record.GB_BASE_INDENT)
+        output += " " * Record.GB_BASE_INDENT
+        taxonomy_info = ""
+        for tax in self.taxonomy:
+            taxonomy_info += f"{tax}; "
+        # replace the ; at the end with a period
+        taxonomy_info = taxonomy_info[:-2]
+        taxonomy_info += "."
+        output += _wrapped_genbank(taxonomy_info, Record.GB_BASE_INDENT)
+
+        return output
+
+    def _comment_line(self):
+        """Output for the COMMENT lines (PRIVATE)."""
+        output = ""
+        if self.comment:
+            output += Record.BASE_FORMAT % "COMMENT"
+            output += _indent_genbank(self.comment, Record.GB_BASE_INDENT)
+        return output
+
+    def _features_line(self):
+        """Output for the FEATURES line (PRIVATE)."""
+        output = ""
+        if len(self.features) > 0:
+            output += Record.BASE_FEATURE_FORMAT % "FEATURES"
+            output += "Location/Qualifiers\n"
+        return output
+
+    def _base_count_line(self):
+        """Output for the BASE COUNT line with base information (PRIVATE)."""
+        output = ""
+        if self.base_counts:
+            output += Record.BASE_FORMAT % "BASE COUNT  "
+            # split up the base counts into their individual parts
+            count_parts = self.base_counts.split(" ")
+            while "" in count_parts:
+                count_parts.remove("")
+            # deal with the standard case, with a normal origin line
+            # like: 474 a    356 c    428 g    364 t
+            if len(count_parts) % 2 == 0:
+                while len(count_parts) > 0:
+                    count_info = count_parts.pop(0)
+                    count_type = count_parts.pop(0)
+
+                    output += f"{count_info:>7} {count_type}"
+            # deal with ugly ORIGIN lines like:
+            # 1311257 a2224835 c2190093 g1309889 t
+            # by just outputting the raw information
+            else:
+                output += self.base_counts
+            output += "\n"
+        return output
+
+    def _origin_line(self):
+        """Output for the ORIGIN line (PRIVATE)."""
+        output = ""
+        # only output the ORIGIN line if we have a sequence
+        if self.sequence:
+            output += Record.BASE_FORMAT % "ORIGIN"
+            if self.origin:
+                output += _wrapped_genbank(self.origin, Record.GB_BASE_INDENT)
+            else:
+                output += "\n"
+        return output
+
+    def _sequence_line(self):
+        """Output for all of the sequence (PRIVATE)."""
+        output = ""
+        if self.sequence:
+            cur_seq_pos = 0
+            while cur_seq_pos < len(self.sequence):
+                output += Record.SEQUENCE_FORMAT % str(cur_seq_pos + 1)
+
+                for section in range(6):
+                    start_pos = cur_seq_pos + section * 10
+                    end_pos = start_pos + 10
+                    seq_section = self.sequence[start_pos:end_pos]
+                    output += f" {seq_section.lower()}"
+
+                    # stop looping if we are out of sequence
+                    if end_pos > len(self.sequence):
+                        break
+
+                output += "\n"
+                cur_seq_pos += 60
+        return output
+
+    def _wgs_line(self):
+        output = ""
+        if self.wgs:
+            output += Record.BASE_FORMAT % "WGS"
+            output += self.wgs
+        return output
+
+    def _wgs_scafld_line(self):
+        output = ""
+        if self.wgs_scafld:
+            output += Record.BASE_FORMAT % "WGS_SCAFLD"
+            output += self.wgs_scafld
+        return output
+
+    def _contig_line(self):
+        """Output for CONTIG location information from RefSeq (PRIVATE)."""
+        output = ""
+        if self.contig:
+            output += Record.BASE_FORMAT % "CONTIG"
+            output += _wrapped_genbank(
+                self.contig, Record.GB_BASE_INDENT, split_char=","
+            )
+        return output
+
+
+class Reference:
+    """Hold information from a GenBank reference.
+
+    Attributes:
+     - number - The number of the reference in the listing of references.
+     - bases - The bases in the sequence the reference refers to.
+     - authors - String with all of the authors.
+     - consrtm - Consortium the authors belong to.
+     - title - The title of the reference.
+     - journal - Information about the journal where the reference appeared.
+     - medline_id - The medline id for the reference.
+     - pubmed_id - The pubmed_id for the reference.
+     - remark - Free-form remarks about the reference.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.number = ""
+        self.bases = ""
+        self.authors = ""
+        self.consrtm = ""
+        self.title = ""
+        self.journal = ""
+        self.medline_id = ""
+        self.pubmed_id = ""
+        self.remark = ""
+
+    def __str__(self):
+        """Convert the reference to a GenBank format string."""
+        output = self._reference_line()
+        output += self._authors_line()
+        output += self._consrtm_line()
+        output += self._title_line()
+        output += self._journal_line()
+        output += self._medline_line()
+        output += self._pubmed_line()
+        output += self._remark_line()
+
+        return output
+
+    def _reference_line(self):
+        """Output for REFERENCE lines (PRIVATE)."""
+        output = Record.BASE_FORMAT % "REFERENCE"
+        if self.number:
+            if self.bases:
+                output += "%-3s" % self.number
+                output += f"{self.bases}"
+            else:
+                output += f"{self.number}"
+
+        output += "\n"
+        return output
+
+    def _authors_line(self):
+        """Output for AUTHORS information (PRIVATE)."""
+        output = ""
+        if self.authors:
+            output += Record.INTERNAL_FORMAT % "AUTHORS"
+            output += _wrapped_genbank(self.authors, Record.GB_BASE_INDENT)
+        return output
+
+    def _consrtm_line(self):
+        """Output for CONSRTM information (PRIVATE)."""
+        output = ""
+        if self.consrtm:
+            output += Record.INTERNAL_FORMAT % "CONSRTM"
+            output += _wrapped_genbank(self.consrtm, Record.GB_BASE_INDENT)
+        return output
+
+    def _title_line(self):
+        """Output for TITLE information (PRIVATE)."""
+        output = ""
+        if self.title:
+            output += Record.INTERNAL_FORMAT % "TITLE"
+            output += _wrapped_genbank(self.title, Record.GB_BASE_INDENT)
+        return output
+
+    def _journal_line(self):
+        """Output for JOURNAL information (PRIVATE)."""
+        output = ""
+        if self.journal:
+            output += Record.INTERNAL_FORMAT % "JOURNAL"
+            output += _wrapped_genbank(self.journal, Record.GB_BASE_INDENT)
+        return output
+
+    def _medline_line(self):
+        """Output for MEDLINE information (PRIVATE)."""
+        output = ""
+        if self.medline_id:
+            output += Record.INTERNAL_FORMAT % "MEDLINE"
+            output += self.medline_id + "\n"
+        return output
+
+    def _pubmed_line(self):
+        """Output for PUBMED information (PRIVATE)."""
+        output = ""
+        if self.pubmed_id:
+            output += Record.OTHER_INTERNAL_FORMAT % "PUBMED"
+            output += self.pubmed_id + "\n"
+        return output
+
+    def _remark_line(self):
+        """Output for REMARK information (PRIVATE)."""
+        output = ""
+        if self.remark:
+            output += Record.INTERNAL_FORMAT % "REMARK"
+            output += _wrapped_genbank(self.remark, Record.GB_BASE_INDENT)
+        return output
+
+
+class Feature:
+    """Hold information about a Feature in the Feature Table of GenBank record.
+
+    Attributes:
+     - key - The key name of the feature (ie. source)
+     - location - The string specifying the location of the feature.
+     - qualifiers - A list of Qualifier objects in the feature.
+
+    """
+
+    def __init__(self, key="", location=""):
+        """Initialize the class."""
+        self.key = key
+        self.location = location
+        self.qualifiers = []
+
+    def __repr__(self):
+        """Representation of the object for debugging or logging."""
+        return f"Feature(key={self.key!r}, location={self.location!r})"
+
+    def __str__(self):
+        """Return feature as a GenBank format string."""
+        output = Record.INTERNAL_FEATURE_FORMAT % self.key
+        output += _wrapped_genbank(
+            self.location, Record.GB_FEATURE_INDENT, split_char=","
+        )
+        for qualifier in self.qualifiers:
+            output += str(qualifier)
+        return output
+
+
+class Qualifier:
+    """Hold information about a qualifier in a GenBank feature.
+
+    Attributes:
+     - key - The key name of the qualifier (ie. /organism=)
+     - value - The value of the qualifier ("Dictyostelium discoideum").
+
+    """
+
+    def __init__(self, key="", value=""):
+        """Initialize the class."""
+        self.key = key
+        self.value = value
+
+    def __repr__(self):
+        """Representation of the object for debugging or logging."""
+        return f"Qualifier(key={self.key!r}, value={self.value!r})"
+
+    def __str__(self):
+        """Return feature qualifier as a GenBank format string."""
+        output = " " * Record.GB_FEATURE_INDENT
+        # determine whether we can wrap on spaces
+        space_wrap = 1
+        for no_space_key in Bio.GenBank._BaseGenBankConsumer.remove_space_keys:
+            if no_space_key in self.key:
+                space_wrap = 0
+        # return double quotes as-is, leave it to the user to escape them
+        return output + _wrapped_genbank(
+            self.key + self.value, Record.GB_FEATURE_INDENT, space_wrap
+        )

.venv_haddock/lib/python3.12/site-packages/Bio/GenBank/Scanner.py

@@ -0,0 +1,1929 @@
+# Copyright 2007-2017 by Peter Cock.  All rights reserved.
+# Revisions copyright 2010 by Uri Laserson.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+"""Internal code for parsing GenBank and EMBL files (PRIVATE).
+
+This code is NOT intended for direct use.  It provides a basic scanner
+(for use with a event consumer such as Bio.GenBank._FeatureConsumer)
+to parse a GenBank or EMBL file (with their shared INSDC feature table).
+
+It is used by Bio.GenBank to parse GenBank files
+It is also used by Bio.SeqIO to parse GenBank and EMBL files
+
+Feature Table Documentation:
+
+- http://www.insdc.org/files/feature_table.html
+- http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
+- ftp://ftp.ncbi.nih.gov/genbank/docs/
+"""
+# 17-MAR-2009: added wgs, wgs_scafld for GenBank whole genome shotgun master records.
+# These are GenBank files that summarize the content of a project, and provide lists of
+# scaffold and contig files in the project. These will be in annotations['wgs'] and
+# annotations['wgs_scafld']. These GenBank files do not have sequences. See
+# http://groups.google.com/group/bionet.molbio.genbank/browse_thread/thread/51fb88bf39e7dc36
+# http://is.gd/nNgk
+# for more details of this format, and an example.
+# Added by Ying Huang & Iddo Friedberg
+
+import re
+import sys
+import warnings
+from collections import defaultdict
+
+from Bio import BiopythonParserWarning
+from Bio.File import as_handle
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+class InsdcScanner:
+    """Basic functions for breaking up a GenBank/EMBL file into sub sections.
+
+    The International Nucleotide Sequence Database Collaboration (INSDC)
+    between the DDBJ, EMBL, and GenBank.  These organisations all use the
+    same "Feature Table" layout in their plain text flat file formats.
+
+    However, the header and sequence sections of an EMBL file are very
+    different in layout to those produced by GenBank/DDBJ.
+    """
+
+    # These constants get redefined with sensible values in the sub classes:
+    RECORD_START = "XXX"  # "LOCUS       " or "ID   "
+    HEADER_WIDTH = 3  # 12 or 5
+    FEATURE_START_MARKERS = ["XXX***FEATURES***XXX"]
+    FEATURE_END_MARKERS = ["XXX***END FEATURES***XXX"]
+    FEATURE_QUALIFIER_INDENT = 0
+    FEATURE_QUALIFIER_SPACER = ""
+    SEQUENCE_HEADERS = ["XXX"]  # with right hand side spaces removed
+
+    def __init__(self, debug=0):
+        """Initialize the class."""
+        assert len(self.RECORD_START) == self.HEADER_WIDTH
+        for marker in self.SEQUENCE_HEADERS:
+            assert marker == marker.rstrip()
+        assert len(self.FEATURE_QUALIFIER_SPACER) == self.FEATURE_QUALIFIER_INDENT
+        self.debug = debug
+        self.handle = None
+        self.line = None
+
+    def set_handle(self, handle):
+        """Set the handle attribute."""
+        self.handle = handle
+        self.line = ""
+
+    def find_start(self):
+        """Read in lines until find the ID/LOCUS line, which is returned.
+
+        Any preamble (such as the header used by the NCBI on ``*.seq.gz`` archives)
+        will we ignored.
+        """
+        while True:
+            if self.line:
+                line = self.line
+                self.line = ""
+            else:
+                line = self.handle.readline()
+            if not line:
+                if self.debug:
+                    print("End of file")
+                return None
+            if isinstance(line[0], int):
+                # Same exception as for FASTQ files
+                raise ValueError("Is this handle in binary mode not text mode?")
+            if line[: self.HEADER_WIDTH] == self.RECORD_START:
+                if self.debug > 1:
+                    print("Found the start of a record:\n" + line)
+                break
+            line = line.rstrip()
+            if line == "//":
+                if self.debug > 1:
+                    print("Skipping // marking end of last record")
+            elif line == "":
+                if self.debug > 1:
+                    print("Skipping blank line before record")
+            else:
+                # Ignore any header before the first ID/LOCUS line.
+                if self.debug > 1:
+                    print("Skipping header line before record:\n" + line)
+        self.line = line
+        return line
+
+    def parse_header(self):
+        """Return list of strings making up the header.
+
+        New line characters are removed.
+
+        Assumes you have just read in the ID/LOCUS line.
+        """
+        if self.line[: self.HEADER_WIDTH] != self.RECORD_START:
+            raise ValueError("Not at start of record")
+
+        header_lines = []
+        while True:
+            line = self.handle.readline()
+            if not line:
+                raise ValueError("Premature end of line during sequence data")
+            line = line.rstrip()
+            if line in self.FEATURE_START_MARKERS:
+                if self.debug:
+                    print("Found feature table")
+                break
+            # if line[:self.HEADER_WIDTH]==self.FEATURE_START_MARKER[:self.HEADER_WIDTH]:
+            #    if self.debug : print("Found header table (?)")
+            #    break
+            if line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
+                if self.debug:
+                    print("Found start of sequence")
+                break
+            if line == "//":
+                raise ValueError("Premature end of sequence data marker '//' found")
+            header_lines.append(line)
+        self.line = line
+        return header_lines
+
+    def parse_features(self, skip=False):
+        """Return list of tuples for the features (if present).
+
+        Each feature is returned as a tuple (key, location, qualifiers)
+        where key and location are strings (e.g. "CDS" and
+        "complement(join(490883..490885,1..879))") while qualifiers
+        is a list of two string tuples (feature qualifier keys and values).
+
+        Assumes you have already read to the start of the features table.
+        """
+        if self.line.rstrip() not in self.FEATURE_START_MARKERS:
+            if self.debug:
+                print("Didn't find any feature table")
+            return []
+
+        while self.line.rstrip() in self.FEATURE_START_MARKERS:
+            self.line = self.handle.readline()
+
+        features = []
+        line = self.line
+        while True:
+            if not line:
+                raise ValueError("Premature end of line during features table")
+            if line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
+                if self.debug:
+                    print("Found start of sequence")
+                break
+            line = line.rstrip()
+            if line == "//":
+                raise ValueError("Premature end of features table, marker '//' found")
+            if line in self.FEATURE_END_MARKERS:
+                if self.debug:
+                    print("Found end of features")
+                line = self.handle.readline()
+                break
+            if line[2 : self.FEATURE_QUALIFIER_INDENT].strip() == "":
+                # This is an empty feature line between qualifiers. Empty
+                # feature lines within qualifiers are handled below (ignored).
+                line = self.handle.readline()
+                continue
+            if len(line) < self.FEATURE_QUALIFIER_INDENT:
+                warnings.warn(
+                    f"line too short to contain a feature: {line!r}",
+                    BiopythonParserWarning,
+                )
+                line = self.handle.readline()
+                continue
+
+            if skip:
+                line = self.handle.readline()
+                while (
+                    line[: self.FEATURE_QUALIFIER_INDENT]
+                    == self.FEATURE_QUALIFIER_SPACER
+                ):
+                    line = self.handle.readline()
+            else:
+                # Build up a list of the lines making up this feature:
+                if (
+                    line[self.FEATURE_QUALIFIER_INDENT] != " "
+                    and " " in line[self.FEATURE_QUALIFIER_INDENT :]
+                ):
+                    # The feature table design enforces a length limit on the feature keys.
+                    # Some third party files (e.g. IGMT's EMBL like files) solve this by
+                    # over indenting the location and qualifiers.
+                    feature_key, line = line[2:].strip().split(None, 1)
+                    feature_lines = [line]
+                    warnings.warn(
+                        f"Over indented {feature_key} feature?",
+                        BiopythonParserWarning,
+                    )
+                else:
+                    feature_key = line[2 : self.FEATURE_QUALIFIER_INDENT].strip()
+                    feature_lines = [line[self.FEATURE_QUALIFIER_INDENT :]]
+                line = self.handle.readline()
+                while line[
+                    : self.FEATURE_QUALIFIER_INDENT
+                ] == self.FEATURE_QUALIFIER_SPACER or (
+                    line != "" and line.rstrip() == ""
+                ):  # cope with blank lines in the midst of a feature
+                    # Use strip to remove any harmless trailing white space AND and leading
+                    # white space (e.g. out of spec files with too much indentation)
+                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT :].strip())
+                    line = self.handle.readline()
+                features.append(self.parse_feature(feature_key, feature_lines))
+        self.line = line
+        return features
+
+    def parse_feature(self, feature_key, lines):
+        r"""Parse a feature given as a list of strings into a tuple.
+
+        Expects a feature as a list of strings, returns a tuple (key, location,
+        qualifiers)
+
+        For example given this GenBank feature::
+
+             CDS             complement(join(490883..490885,1..879))
+                             /locus_tag="NEQ001"
+                             /note="conserved hypothetical [Methanococcus jannaschii];
+                             COG1583:Uncharacterized ACR; IPR001472:Bipartite nuclear
+                             localization signal; IPR002743: Protein of unknown
+                             function DUF57"
+                             /codon_start=1
+                             /transl_table=11
+                             /product="hypothetical protein"
+                             /protein_id="NP_963295.1"
+                             /db_xref="GI:41614797"
+                             /db_xref="GeneID:2732620"
+                             /translation="MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK
+                             EKYFNFTLIPKKDIIENKRYYLIISSPDKRFIEVLHNKIKDLDIITIGLAQFQLRKTK
+                             KFDPKLRFPWVTITPIVLREGKIVILKGDKYYKVFVKRLEELKKYNLIKKKEPILEEP
+                             IEISLNQIKDGWKIIDVKDRYYDFRNKSFSAFSNWLRDLKEQSLRKYNNFCGKNFYFE
+                             EAIFEGFTFYKTVSIRIRINRGEAVYIGTLWKELNVYRKLDKEEREFYKFLYDCGLGS
+                             LNSMGFGFVNTKKNSAR"
+
+        Then should give input key="CDS" and the rest of the data as a list of strings
+        lines=["complement(join(490883..490885,1..879))", ..., "LNSMGFGFVNTKKNSAR"]
+        where the leading spaces and trailing newlines have been removed.
+
+        Returns tuple containing: (key as string, location string, qualifiers as list)
+        as follows for this example:
+
+        key = "CDS", string
+        location = "complement(join(490883..490885,1..879))", string
+        qualifiers = list of string tuples:
+
+        [('locus_tag', '"NEQ001"'),
+         ('note', '"conserved hypothetical [Methanococcus jannaschii];\nCOG1583:..."'),
+         ('codon_start', '1'),
+         ('transl_table', '11'),
+         ('product', '"hypothetical protein"'),
+         ('protein_id', '"NP_963295.1"'),
+         ('db_xref', '"GI:41614797"'),
+         ('db_xref', '"GeneID:2732620"'),
+         ('translation', '"MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK\nEKYFNFT..."')]
+
+        In the above example, the "note" and "translation" were edited for compactness,
+        and they would contain multiple new line characters (displayed above as \n)
+
+        If a qualifier is quoted (in this case, everything except codon_start and
+        transl_table) then the quotes are NOT removed.
+
+        Note that no whitespace is removed.
+        """
+        # Skip any blank lines
+        iterator = (x for x in lines if x)
+        try:
+            line = next(iterator)
+
+            feature_location = line.strip()
+            while feature_location[-1:] == ",":
+                # Multiline location, still more to come!
+                line = next(iterator)
+                feature_location += line.strip()
+            if feature_location.count("(") > feature_location.count(")"):
+                # Including the prev line in warning would be more explicit,
+                # but this way get one-and-only-one warning shown by default:
+                warnings.warn(
+                    "Non-standard feature line wrapping (didn't break on comma)?",
+                    BiopythonParserWarning,
+                )
+                while feature_location[-1:] == "," or feature_location.count(
+                    "("
+                ) > feature_location.count(")"):
+                    line = next(iterator)
+                    feature_location += line.strip()
+
+            qualifiers = []
+
+            for line_number, line in enumerate(iterator):
+                # check for extra wrapping of the location closing parentheses
+                if line_number == 0 and line.startswith(")"):
+                    feature_location += line.strip()
+                elif line[0] == "/":
+                    # New qualifier
+                    i = line.find("=")
+                    key = line[1:i]  # does not work if i==-1
+                    value = line[i + 1 :]  # we ignore 'value' if i==-1
+                    if i and value.startswith(" ") and value.lstrip().startswith('"'):
+                        warnings.warn(
+                            "White space after equals in qualifier",
+                            BiopythonParserWarning,
+                        )
+                        value = value.lstrip()
+                    if i == -1:
+                        # Qualifier with no key, e.g. /pseudo
+                        key = line[1:]
+                        qualifiers.append((key, None))
+                    elif not value:
+                        # ApE can output /note=
+                        qualifiers.append((key, ""))
+                    elif value == '"':
+                        # One single quote
+                        if self.debug:
+                            print(f"Single quote {key}:{value}")
+                        # DO NOT remove the quote...
+                        qualifiers.append((key, value))
+                    elif value[0] == '"':
+                        # Quoted...
+                        value_list = [value]
+                        while value_list[-1][-1] != '"':
+                            value_list.append(next(iterator))
+                        value = "\n".join(value_list)
+                        # DO NOT remove the quotes...
+                        qualifiers.append((key, value))
+                    else:
+                        # Unquoted
+                        # if debug : print("Unquoted line %s:%s" % (key,value))
+                        qualifiers.append((key, value))
+                else:
+                    # Unquoted continuation
+                    assert len(qualifiers) > 0
+                    assert key == qualifiers[-1][0]
+                    # if debug : print("Unquoted Cont %s:%s" % (key, line))
+                    if qualifiers[-1][1] is None:
+                        raise StopIteration
+                    qualifiers[-1] = (key, qualifiers[-1][1] + "\n" + line)
+            return feature_key, feature_location, qualifiers
+        except StopIteration:
+            # Bummer
+            raise ValueError(
+                "Problem with '%s' feature:\n%s" % (feature_key, "\n".join(lines))
+            ) from None
+
+    def parse_footer(self):
+        """Return a tuple containing a list of any misc strings, and the sequence."""
+        # This is a basic bit of code to scan and discard the sequence,
+        # which was useful when developing the sub classes.
+        if self.line in self.FEATURE_END_MARKERS:
+            while self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
+                self.line = self.handle.readline()
+                if not self.line:
+                    raise ValueError("Premature end of file")
+                self.line = self.line.rstrip()
+
+        if self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
+            raise ValueError("Not at start of sequence")
+        while True:
+            line = self.handle.readline()
+            if not line:
+                raise ValueError("Premature end of line during sequence data")
+            line = line.rstrip()
+            if line == "//":
+                break
+        self.line = line
+        return [], ""  # Dummy values!
+
+    def _feed_first_line(self, consumer, line):
+        """Handle the LOCUS/ID line, passing data to the consumer (PRIVATE).
+
+        This should be implemented by the EMBL / GenBank specific subclass
+
+        Used by the parse_records() and parse() methods.
+        """
+
+    def _feed_header_lines(self, consumer, lines):
+        """Handle the header lines (list of strings), passing data to the consumer (PRIVATE).
+
+        This should be implemented by the EMBL / GenBank specific subclass
+
+        Used by the parse_records() and parse() methods.
+        """
+
+    @staticmethod
+    def _feed_feature_table(consumer, feature_tuples):
+        """Handle the feature table (list of tuples), passing data to the consumer (PRIVATE).
+
+        Used by the parse_records() and parse() methods.
+        """
+        consumer.start_feature_table()
+        for feature_key, location_string, qualifiers in feature_tuples:
+            consumer.feature_key(feature_key)
+            consumer.location(location_string)
+            for q_key, q_value in qualifiers:
+                if q_value is None:
+                    consumer.feature_qualifier(q_key, q_value)
+                else:
+                    consumer.feature_qualifier(q_key, q_value.replace("\n", " "))
+
+    def _feed_misc_lines(self, consumer, lines):
+        """Handle any lines between features and sequence (list of strings), passing data to the consumer (PRIVATE).
+
+        This should be implemented by the EMBL / GenBank specific subclass
+
+        Used by the parse_records() and parse() methods.
+        """
+
+    def feed(self, handle, consumer, do_features=True):
+        """Feed a set of data into the consumer.
+
+        This method is intended for use with the "old" code in Bio.GenBank
+
+        Arguments:
+         - handle - A handle with the information to parse.
+         - consumer - The consumer that should be informed of events.
+         - do_features - Boolean, should the features be parsed?
+           Skipping the features can be much faster.
+
+        Return values:
+         - true  - Passed a record
+         - false - Did not find a record
+
+        """
+        # Should work with both EMBL and GenBank files provided the
+        # equivalent Bio.GenBank._FeatureConsumer methods are called...
+        self.set_handle(handle)
+        if not self.find_start():
+            # Could not find (another) record
+            consumer.data = None
+            return False
+
+        # We use the above class methods to parse the file into a simplified format.
+        # The first line, header lines and any misc lines after the features will be
+        # dealt with by GenBank / EMBL specific derived classes.
+
+        # First line and header:
+        self._feed_first_line(consumer, self.line)
+        self._feed_header_lines(consumer, self.parse_header())
+
+        # Features (common to both EMBL and GenBank):
+        if do_features:
+            self._feed_feature_table(consumer, self.parse_features(skip=False))
+        else:
+            self.parse_features(skip=True)  # ignore the data
+
+        # Footer and sequence
+        misc_lines, sequence_string = self.parse_footer()
+        self._feed_misc_lines(consumer, misc_lines)
+
+        consumer.sequence(sequence_string)
+        # Calls to consumer.base_number() do nothing anyway
+        consumer.record_end("//")
+
+        assert self.line == "//"
+
+        # And we are done
+        return True
+
+    def parse(self, handle, do_features=True):
+        """Return a SeqRecord (with SeqFeatures if do_features=True).
+
+        See also the method parse_records() for use on multi-record files.
+        """
+        from Bio.GenBank import _FeatureConsumer
+        from Bio.GenBank.utils import FeatureValueCleaner
+
+        consumer = _FeatureConsumer(
+            use_fuzziness=1, feature_cleaner=FeatureValueCleaner()
+        )
+
+        if self.feed(handle, consumer, do_features):
+            return consumer.data
+        else:
+            return None
+
+    def parse_records(self, handle, do_features=True):
+        """Parse records, return a SeqRecord object iterator.
+
+        Each record (from the ID/LOCUS line to the // line) becomes a SeqRecord
+
+        The SeqRecord objects include SeqFeatures if do_features=True
+
+        This method is intended for use in Bio.SeqIO
+        """
+        # This is a generator function
+        with as_handle(handle) as handle:
+            while True:
+                record = self.parse(handle, do_features)
+                if record is None:
+                    break
+                if record.id is None:
+                    raise ValueError(
+                        "Failed to parse the record's ID. Invalid ID line?"
+                    )
+                if record.name == "<unknown name>":
+                    raise ValueError(
+                        "Failed to parse the record's name. Invalid ID line?"
+                    )
+                if record.description == "<unknown description>":
+                    raise ValueError("Failed to parse the record's description")
+                yield record
+
+    def parse_cds_features(
+        self, handle, alphabet=None, tags2id=("protein_id", "locus_tag", "product")
+    ):
+        """Parse CDS features, return SeqRecord object iterator.
+
+        Each CDS feature becomes a SeqRecord.
+
+        Arguments:
+         - alphabet - Obsolete, should be left as None.
+         - tags2id  - Tuple of three strings, the feature keys to use
+           for the record id, name and description,
+
+        This method is intended for use in Bio.SeqIO
+
+        """
+        if alphabet is not None:
+            raise ValueError("The alphabet argument is no longer supported")
+        with as_handle(handle) as handle:
+            self.set_handle(handle)
+            while self.find_start():
+                # Got an EMBL or GenBank record...
+                self.parse_header()  # ignore header lines!
+                feature_tuples = self.parse_features()
+                # self.parse_footer() # ignore footer lines!
+                while True:
+                    line = self.handle.readline()
+                    if not line:
+                        break
+                    if line[:2] == "//":
+                        break
+                self.line = line.rstrip()
+
+                # Now go though those features...
+                for key, location_string, qualifiers in feature_tuples:
+                    if key == "CDS":
+                        # Create SeqRecord
+                        # ================
+                        # SeqRecord objects cannot be created with annotations, they
+                        # must be added afterwards.  So create an empty record and
+                        # then populate it:
+                        record = SeqRecord(seq=None)
+                        annotations = record.annotations
+                        annotations["molecule_type"] = "protein"
+                        # Should we add a location object to the annotations?
+                        # I *think* that only makes sense for SeqFeatures with their
+                        # sub features...
+                        annotations["raw_location"] = location_string.replace(" ", "")
+
+                        for qualifier_name, qualifier_data in qualifiers:
+                            if (
+                                qualifier_data is not None
+                                and qualifier_data[0] == '"'
+                                and qualifier_data[-1] == '"'
+                            ):
+                                # Remove quotes
+                                qualifier_data = qualifier_data[1:-1]
+                            # Append the data to the annotation qualifier...
+                            if qualifier_name == "translation":
+                                assert record.seq is None, "Multiple translations!"
+                                record.seq = Seq(qualifier_data.replace("\n", ""))
+                            elif qualifier_name == "db_xref":
+                                # its a list, possibly empty.  Its safe to extend
+                                record.dbxrefs.append(qualifier_data)
+                            else:
+                                if qualifier_data is not None:
+                                    qualifier_data = qualifier_data.replace(
+                                        "\n", " "
+                                    ).replace("  ", " ")
+                                try:
+                                    annotations[qualifier_name] += " " + qualifier_data
+                                except KeyError:
+                                    # Not an addition to existing data, its the first bit
+                                    annotations[qualifier_name] = qualifier_data
+
+                        # Fill in the ID, Name, Description
+                        # =================================
+                        try:
+                            record.id = annotations[tags2id[0]]
+                        except KeyError:
+                            pass
+                        try:
+                            record.name = annotations[tags2id[1]]
+                        except KeyError:
+                            pass
+                        try:
+                            record.description = annotations[tags2id[2]]
+                        except KeyError:
+                            pass
+
+                        yield record
+
+
+class EmblScanner(InsdcScanner):
+    """For extracting chunks of information in EMBL files."""
+
+    RECORD_START = "ID   "
+    HEADER_WIDTH = 5
+    FEATURE_START_MARKERS = ["FH   Key             Location/Qualifiers", "FH"]
+    FEATURE_END_MARKERS = ["XX"]  # XX can also mark the end of many things!
+    FEATURE_QUALIFIER_INDENT = 21
+    FEATURE_QUALIFIER_SPACER = "FT" + " " * (FEATURE_QUALIFIER_INDENT - 2)
+    SEQUENCE_HEADERS = ["SQ", "CO"]  # Remove trailing spaces
+
+    EMBL_INDENT = HEADER_WIDTH
+    EMBL_SPACER = " " * EMBL_INDENT
+
+    def parse_footer(self):
+        """Return a tuple containing a list of any misc strings, and the sequence."""
+        if self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
+            raise ValueError(f"Footer format unexpected: '{self.line}'")
+
+        # Note that the SQ line can be split into several lines...
+        misc_lines = []
+        while self.line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
+            misc_lines.append(self.line)
+            self.line = self.handle.readline()
+            if not self.line:
+                raise ValueError("Premature end of file")
+            self.line = self.line.rstrip()
+
+        if not (
+            self.line[: self.HEADER_WIDTH] == " " * self.HEADER_WIDTH
+            or self.line.strip() == "//"
+        ):
+            raise ValueError(f"Unexpected content after SQ or CO line: {self.line!r}")
+
+        seq_lines = []
+        line = self.line
+        while True:
+            if not line:
+                raise ValueError("Premature end of file in sequence data")
+            line = line.strip()
+            if not line:
+                raise ValueError("Blank line in sequence data")
+            if line == "//":
+                break
+            if self.line[: self.HEADER_WIDTH] != (" " * self.HEADER_WIDTH):
+                raise ValueError(
+                    "Problem with characters in header line, "
+                    " or incorrect header width: " + self.line
+                )
+            # Remove tailing number now, remove spaces later
+            linersplit = line.rsplit(None, 1)
+            if len(linersplit) == 2 and linersplit[1].isdigit():
+                seq_lines.append(linersplit[0])
+            elif line.isdigit():
+                # Special case of final blank line with no bases
+                # just the sequence coordinate
+                pass
+            else:
+                warnings.warn(
+                    "EMBL sequence line missing coordinates", BiopythonParserWarning
+                )
+                seq_lines.append(line)
+            line = self.handle.readline()
+        self.line = line
+        return misc_lines, "".join(seq_lines).replace(" ", "")
+
+    def _feed_first_line(self, consumer, line):
+        assert line[: self.HEADER_WIDTH].rstrip() == "ID"
+        if line[self.HEADER_WIDTH :].count(";") == 6:
+            # Looks like the semi colon separated style introduced in 2006
+            self._feed_first_line_new(consumer, line)
+        elif line[self.HEADER_WIDTH :].count(";") == 3:
+            if line.rstrip().endswith(" SQ"):
+                # EMBL-bank patent data
+                self._feed_first_line_patents(consumer, line)
+            else:
+                # Looks like the pre 2006 style
+                self._feed_first_line_old(consumer, line)
+        elif line[self.HEADER_WIDTH :].count(";") == 2:
+            # Looks like KIKO patent data
+            self._feed_first_line_patents_kipo(consumer, line)
+        else:
+            raise ValueError("Did not recognise the ID line layout:\n" + line)
+
+    def _feed_first_line_patents(self, consumer, line):
+        # Old style EMBL patent records where ID line ended SQ
+        # Not 100% sure that PRT here is really molecule type and
+        # not the data file division...
+        #
+        # Either Non-Redundant Level 1 database records,
+        # ID <accession>; <molecule type>; <non-redundant level 1>; <cluster size L1>
+        # e.g. ID   NRP_AX000635; PRT; NR1; 15 SQ
+        #
+        # Or, Non-Redundant Level 2 database records:
+        # ID <L2-accession>; <molecule type>; <non-redundant level 2>; <cluster size L2>
+        # e.g. ID   NRP0000016E; PRT; NR2; 5 SQ
+        # e.g. ID   NRP_AX000635; PRT; NR1; 15 SQ
+        fields = [
+            data.strip() for data in line[self.HEADER_WIDTH :].strip()[:-3].split(";")
+        ]
+        assert len(fields) == 4
+        consumer.locus(fields[0])
+        consumer.residue_type(fields[1])  # semi-redundant
+        consumer.data_file_division(fields[2])
+        # TODO - Record cluster size?
+
+    def _feed_first_line_patents_kipo(self, consumer, line):
+        # EMBL format patent sequence from KIPO, e.g.
+        # ftp://ftp.ebi.ac.uk/pub/databases/patentdata/kipo_prt.dat.gz
+        #
+        # e.g. ID   DI500001       STANDARD;      PRT;   111 AA.
+        #
+        # This follows the style of _feed_first_line_old
+        assert line[: self.HEADER_WIDTH].rstrip() == "ID"
+        fields = [line[self.HEADER_WIDTH :].split(None, 1)[0]]
+        fields.extend(line[self.HEADER_WIDTH :].split(None, 1)[1].split(";"))
+        fields = [entry.strip() for entry in fields]
+        """
+        The tokens represent:
+
+           0. Primary accession number
+           (space sep)
+           1. ??? (e.g. standard)
+           (semi-colon)
+           2. Molecule type (protein)? Division? Always 'PRT'
+           3. Sequence length (e.g. '111 AA.')
+        """
+        consumer.locus(fields[0])  # Should we also call the accession consumer?
+        # consumer.molecule_type(fields[2])
+        self._feed_seq_length(consumer, fields[3])
+
+    def _feed_first_line_old(self, consumer, line):
+        # Expects an ID line in the style before 2006, e.g.
+        # ID   SC10H5 standard; DNA; PRO; 4870 BP.
+        # ID   BSUB9999   standard; circular DNA; PRO; 4214630 BP.
+        assert line[: self.HEADER_WIDTH].rstrip() == "ID"
+        fields = [line[self.HEADER_WIDTH :].split(None, 1)[0]]
+        fields.extend(line[self.HEADER_WIDTH :].split(None, 1)[1].split(";"))
+        fields = [entry.strip() for entry in fields]
+        """
+        The tokens represent:
+
+           0. Primary accession number
+           (space sep)
+           1. ??? (e.g. standard)
+           (semi-colon)
+           2. Topology and/or Molecule type (e.g. 'circular DNA' or 'DNA')
+           3. Taxonomic division (e.g. 'PRO')
+           4. Sequence length (e.g. '4639675 BP.')
+
+        """
+        consumer.locus(fields[0])  # Should we also call the accession consumer?
+        consumer.residue_type(fields[2])
+        if "circular" in fields[2]:
+            consumer.topology("circular")
+            consumer.molecule_type(fields[2].replace("circular", "").strip())
+        elif "linear" in fields[2]:
+            consumer.topology("linear")
+            consumer.molecule_type(fields[2].replace("linear", "").strip())
+        else:
+            consumer.molecule_type(fields[2].strip())
+        consumer.data_file_division(fields[3])
+        self._feed_seq_length(consumer, fields[4])
+
+    def _feed_first_line_new(self, consumer, line):
+        # Expects an ID line in the style introduced in 2006, e.g.
+        # ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
+        # ID   CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP.
+        assert line[: self.HEADER_WIDTH].rstrip() == "ID"
+        fields = [data.strip() for data in line[self.HEADER_WIDTH :].strip().split(";")]
+        assert len(fields) == 7
+        """
+        The tokens represent:
+
+           0. Primary accession number
+           1. Sequence version number
+           2. Topology: 'circular' or 'linear'
+           3. Molecule type (e.g. 'genomic DNA')
+           4. Data class (e.g. 'STD')
+           5. Taxonomic division (e.g. 'PRO')
+           6. Sequence length (e.g. '4639675 BP.')
+
+        """
+
+        consumer.locus(fields[0])
+
+        # Call the accession consumer now, to make sure we record
+        # something as the record.id, in case there is no AC line
+        consumer.accession(fields[0])
+
+        # TODO - How to deal with the version field?  At the moment the consumer
+        # will try and use this for the ID which isn't ideal for EMBL files.
+        version_parts = fields[1].split()
+        if (
+            len(version_parts) == 2
+            and version_parts[0] == "SV"
+            and version_parts[1].isdigit()
+        ):
+            consumer.version_suffix(version_parts[1])
+
+        # Based on how the old GenBank parser worked, merge these two:
+        consumer.residue_type(" ".join(fields[2:4]))  # Semi-obsolete
+
+        consumer.topology(fields[2])
+        consumer.molecule_type(fields[3])
+
+        # consumer.xxx(fields[4]) # TODO - What should we do with the data class?
+
+        consumer.data_file_division(fields[5])
+
+        self._feed_seq_length(consumer, fields[6])
+
+    @staticmethod
+    def _feed_seq_length(consumer, text):
+        length_parts = text.split()
+        assert len(length_parts) == 2, f"Invalid sequence length string {text!r}"
+        assert length_parts[1].upper() in ["BP", "BP.", "AA", "AA."]
+        consumer.size(length_parts[0])
+
+    def _feed_header_lines(self, consumer, lines):
+        consumer_dict = {
+            "AC": "accession",
+            "SV": "version",  # SV line removed in June 2006, now part of ID line
+            "DE": "definition",
+            # 'RN' : 'reference_num',
+            # 'RC' : reference comment... TODO
+            # 'RP' : 'reference_bases',
+            # 'RX' : reference cross reference... DOI or Pubmed
+            "RG": "consrtm",  # optional consortium
+            # 'RA' : 'authors',
+            # 'RT' : 'title',
+            "RL": "journal",
+            "OS": "organism",
+            "OC": "taxonomy",
+            # 'DR' : data reference
+            "CC": "comment",
+            # 'XX' : splitter
+        }
+        # We have to handle the following specially:
+        # RX (depending on reference type...)
+        for line in lines:
+            line_type = line[: self.EMBL_INDENT].strip()
+            data = line[self.EMBL_INDENT :].strip()
+            if line_type == "XX":
+                pass
+            elif line_type == "RN":
+                # Reformat reference numbers for the GenBank based consumer
+                # e.g. '[1]' becomes '1'
+                if data[0] == "[" and data[-1] == "]":
+                    data = data[1:-1]
+                consumer.reference_num(data)
+            elif line_type == "RP":
+                if data.strip() == "[-]":
+                    # Patent EMBL files from KIPO just use: RN  [-]
+                    pass
+                else:
+                    # Reformat reference numbers for the GenBank based consumer
+                    # e.g. '1-4639675' becomes '(bases 1 to 4639675)'
+                    # and '160-550, 904-1055' becomes '(bases 160 to 550; 904 to 1055)'
+                    # Note could be multi-line, and end with a comma
+                    parts = [
+                        bases.replace("-", " to ").strip()
+                        for bases in data.split(",")
+                        if bases.strip()
+                    ]
+                    consumer.reference_bases(f"(bases {'; '.join(parts)})")
+            elif line_type == "RT":
+                # Remove the enclosing quotes and trailing semi colon.
+                # Note the title can be split over multiple lines.
+                if data.startswith('"'):
+                    data = data[1:]
+                if data.endswith('";'):
+                    data = data[:-2]
+                consumer.title(data)
+            elif line_type == "RX":
+                # EMBL support three reference types at the moment:
+                # - PUBMED    PUBMED bibliographic database (NLM)
+                # - DOI       Digital Object Identifier (International DOI Foundation)
+                # - AGRICOLA  US National Agriculture Library (NAL) of the US Department
+                #             of Agriculture (USDA)
+                #
+                # Format:
+                # RX  resource_identifier; identifier.
+                #
+                # e.g.
+                # RX   DOI; 10.1016/0024-3205(83)90010-3.
+                # RX   PUBMED; 264242.
+                #
+                # Currently our reference object only supports PUBMED and MEDLINE
+                # (as these were in GenBank files?).
+                key, value = data.split(";", 1)
+                if value.endswith("."):
+                    value = value[:-1]
+                value = value.strip()
+                if key == "PUBMED":
+                    consumer.pubmed_id(value)
+                # TODO - Handle other reference types (here and in BioSQL bindings)
+            elif line_type == "CC":
+                # Have to pass a list of strings for this one (not just a string)
+                consumer.comment([data])
+            elif line_type == "DR":
+                # Database Cross-reference, format:
+                # DR   database_identifier; primary_identifier; secondary_identifier.
+                #
+                # e.g.
+                # DR   MGI; 98599; Tcrb-V4.
+                #
+                # TODO - How should we store any secondary identifier?
+                parts = data.rstrip(".").split(";")
+                # Turn it into "database_identifier:primary_identifier" to
+                # mimic the GenBank parser. e.g. "MGI:98599"
+                if len(parts) == 1:
+                    warnings.warn(
+                        "Malformed DR line in EMBL file.", BiopythonParserWarning
+                    )
+                else:
+                    consumer.dblink(f"{parts[0].strip()}:{parts[1].strip()}")
+            elif line_type == "RA":
+                # Remove trailing ; at end of authors list
+                consumer.authors(data.rstrip(";"))
+            elif line_type == "PR":
+                # In the EMBL patent files, this is a PR (PRiority) line which
+                # provides the earliest active priority within the family.
+                # The priority  number comes first, followed by the priority date.
+                #
+                # e.g.
+                # PR   JP19990377484 16-DEC-1999
+                #
+                # However, in most EMBL files this is a PR (PRoject) line which
+                # gives the BioProject reference number.
+                #
+                # e.g.
+                # PR   Project:PRJNA60715;
+                #
+                # In GenBank files this corresponds to the old PROJECT line
+                # which was later replaced with the DBLINK line.
+                if data.startswith("Project:"):
+                    # Remove trailing ; at end of the project reference
+                    consumer.project(data.rstrip(";"))
+            elif line_type == "KW":
+                consumer.keywords(data.rstrip(";"))
+            elif line_type in consumer_dict:
+                # Its a semi-automatic entry!
+                getattr(consumer, consumer_dict[line_type])(data)
+            else:
+                if self.debug:
+                    print(f"Ignoring EMBL header line:\n{line}")
+
+    def _feed_misc_lines(self, consumer, lines):
+        # TODO - Should we do something with the information on the SQ line(s)?
+        lines.append("")
+        line_iter = iter(lines)
+        try:
+            for line in line_iter:
+                if line.startswith("CO   "):
+                    line = line[5:].strip()
+                    contig_location = line
+                    while True:
+                        line = next(line_iter)
+                        if not line:
+                            break
+                        elif line.startswith("CO   "):
+                            # Don't need to preserve the whitespace here.
+                            contig_location += line[5:].strip()
+                        else:
+                            raise ValueError(
+                                "Expected CO (contig) continuation line, got:\n" + line
+                            )
+                    consumer.contig_location(contig_location)
+                if line.startswith("SQ   Sequence "):
+                    # e.g.
+                    # SQ   Sequence 219 BP; 82 A; 48 C; 33 G; 45 T; 11 other;
+                    #
+                    # Or, EMBL-bank patent, e.g.
+                    # SQ   Sequence 465 AA; 3963407aa91d3a0d622fec679a4524e0; MD5;
+                    self._feed_seq_length(
+                        consumer, line[14:].rstrip().rstrip(";").split(";", 1)[0]
+                    )
+                    # TODO - Record the checksum etc?
+            return
+        except StopIteration:
+            raise ValueError("Problem in misc lines before sequence") from None
+
+
+class _ImgtScanner(EmblScanner):
+    """For extracting chunks of information in IMGT (EMBL like) files (PRIVATE).
+
+    IMGT files are like EMBL files but in order to allow longer feature types
+    the features should be indented by 25 characters not 21 characters. In
+    practice the IMGT flat files tend to use either 21 or 25 characters, so we
+    must cope with both.
+
+    This is private to encourage use of Bio.SeqIO rather than Bio.GenBank.
+    """
+
+    FEATURE_START_MARKERS = [
+        "FH   Key             Location/Qualifiers",
+        "FH   Key             Location/Qualifiers (from EMBL)",
+        "FH   Key                 Location/Qualifiers",
+        "FH",
+    ]
+
+    def _feed_first_line(self, consumer, line):
+        assert line[: self.HEADER_WIDTH].rstrip() == "ID"
+        if line[self.HEADER_WIDTH :].count(";") != 5:
+            # Assume its an older EMBL-like line,
+            return EmblScanner._feed_first_line(self, consumer, line)
+        # Otherwise assume its the new (circa 2016) IMGT style
+        # as used in the IPD-IMGT/HLA Database
+        #
+        # https://github.com/ANHIG/IMGTHLA/
+        #
+        # The key changes post 3.16 are the addition of an SV value
+        # to the ID line, these additions should make the format more
+        # similar to the ENA style.
+        #
+        # ID   HLA00001   standard; DNA; HUM; 3503 BP.
+        #
+        # becomes
+        #
+        # ID   HLA00001; SV 1; standard; DNA; HUM; 3503 BP.
+        fields = [data.strip() for data in line[self.HEADER_WIDTH :].strip().split(";")]
+        assert len(fields) == 6
+        """
+        The tokens represent:
+
+           0. Primary accession number (eg 'HLA00001')
+           1. Sequence version number (eg 'SV 1')
+           2. ??? eg 'standard'
+           3. Molecule type (e.g. 'DNA')
+           4. Taxonomic division (e.g. 'HUM')
+           5. Sequence length (e.g. '3503 BP.')
+        """
+        consumer.locus(fields[0])
+
+        # See TODO on the EMBL _feed_first_line_new about version field
+        version_parts = fields[1].split()
+        if (
+            len(version_parts) == 2
+            and version_parts[0] == "SV"
+            and version_parts[1].isdigit()
+        ):
+            consumer.version_suffix(version_parts[1])
+
+        consumer.residue_type(fields[3])
+        if "circular" in fields[3]:
+            consumer.topology("circular")
+            consumer.molecule_type(fields[3].replace("circular", "").strip())
+        elif "linear" in fields[3]:
+            consumer.topology("linear")
+            consumer.molecule_type(fields[3].replace("linear", "").strip())
+        else:
+            consumer.molecule_type(fields[3].strip())
+        consumer.data_file_division(fields[4])
+        self._feed_seq_length(consumer, fields[5])
+
+    def parse_features(self, skip=False):
+        """Return list of tuples for the features (if present).
+
+        Each feature is returned as a tuple (key, location, qualifiers)
+        where key and location are strings (e.g. "CDS" and
+        "complement(join(490883..490885,1..879))") while qualifiers
+        is a list of two string tuples (feature qualifier keys and values).
+
+        Assumes you have already read to the start of the features table.
+        """
+        if self.line.rstrip() not in self.FEATURE_START_MARKERS:
+            if self.debug:
+                print("Didn't find any feature table")
+            return []
+
+        while self.line.rstrip() in self.FEATURE_START_MARKERS:
+            self.line = self.handle.readline()
+
+        bad_position_re = re.compile(r"([0-9]+)>")
+
+        features = []
+        line = self.line
+        while True:
+            if not line:
+                raise ValueError("Premature end of line during features table")
+            if line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
+                if self.debug:
+                    print("Found start of sequence")
+                break
+            line = line.rstrip()
+            if line == "//":
+                raise ValueError("Premature end of features table, marker '//' found")
+            if line in self.FEATURE_END_MARKERS:
+                if self.debug:
+                    print("Found end of features")
+                line = self.handle.readline()
+                break
+            if line[2 : self.FEATURE_QUALIFIER_INDENT].strip() == "":
+                # This is an empty feature line between qualifiers. Empty
+                # feature lines within qualifiers are handled below (ignored).
+                line = self.handle.readline()
+                continue
+
+            if skip:
+                line = self.handle.readline()
+                while (
+                    line[: self.FEATURE_QUALIFIER_INDENT]
+                    == self.FEATURE_QUALIFIER_SPACER
+                ):
+                    line = self.handle.readline()
+            else:
+                assert line[:2] == "FT"
+                try:
+                    feature_key, location_start = line[2:].strip().split()
+                except ValueError:
+                    # e.g. "FT   TRANSMEMBRANE-REGION2163..2240\n"
+                    # Assume indent of 25 as per IMGT spec, with the location
+                    # start in column 26 (one-based).
+                    feature_key = line[2:25].strip()
+                    location_start = line[25:].strip()
+                feature_lines = [location_start]
+                line = self.handle.readline()
+                while (
+                    line[: self.FEATURE_QUALIFIER_INDENT]
+                    == self.FEATURE_QUALIFIER_SPACER
+                    or line.rstrip() == ""
+                ):  # cope with blank lines in the midst of a feature
+                    # Use strip to remove any harmless trailing white space AND and leading
+                    # white space (copes with 21 or 26 indents and orther variants)
+                    assert line[:2] == "FT"
+                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT :].strip())
+                    line = self.handle.readline()
+                feature_key, location, qualifiers = self.parse_feature(
+                    feature_key, feature_lines
+                )
+                # Try to handle known problems with IMGT locations here:
+                if ">" in location:
+                    # Nasty hack for common IMGT bug, should be >123 not 123>
+                    # in a location string. At least here the meaning is clear,
+                    # and since it is so common I don't want to issue a warning
+                    # warnings.warn("Feature location %s is invalid, "
+                    #              "moving greater than sign before position"
+                    #              % location, BiopythonParserWarning)
+                    location = bad_position_re.sub(r">\1", location)
+                features.append((feature_key, location, qualifiers))
+        self.line = line
+        return features
+
+
+class GenBankScanner(InsdcScanner):
+    """For extracting chunks of information in GenBank files."""
+
+    RECORD_START = "LOCUS       "
+    HEADER_WIDTH = 12
+    FEATURE_START_MARKERS = ["FEATURES             Location/Qualifiers", "FEATURES"]
+    FEATURE_END_MARKERS: list[str] = []
+    FEATURE_QUALIFIER_INDENT = 21
+    FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT
+    SEQUENCE_HEADERS = [
+        "CONTIG",
+        "ORIGIN",
+        "BASE COUNT",
+        "WGS",
+        "TSA",
+        "TLS",
+    ]  # trailing spaces removed
+
+    GENBANK_INDENT = HEADER_WIDTH
+    GENBANK_SPACER = " " * GENBANK_INDENT
+
+    STRUCTURED_COMMENT_START = "-START##"
+    STRUCTURED_COMMENT_END = "-END##"
+    STRUCTURED_COMMENT_DELIM = " :: "
+
+    def parse_footer(self):
+        """Return a tuple containing a list of any misc strings, and the sequence."""
+        if self.line[: self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS:
+            raise ValueError(f"Footer format unexpected:  '{self.line}'")
+
+        misc_lines = []
+        while (
+            self.line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS
+            or self.line[: self.HEADER_WIDTH] == " " * self.HEADER_WIDTH
+            or "WGS" == self.line[:3]
+        ):
+            misc_lines.append(self.line.rstrip())
+            self.line = self.handle.readline()
+            if not self.line:
+                raise ValueError("Premature end of file")
+
+        if self.line[: self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS:
+            raise ValueError(f"Eh? '{self.line}'")
+
+        # Now just consume the sequence lines until reach the // marker
+        # or a CONTIG line
+        seq_lines = []
+        line = self.line
+        while True:
+            if not line:
+                warnings.warn(
+                    "Premature end of file in sequence data", BiopythonParserWarning
+                )
+                line = "//"
+                break
+            line = line.rstrip()
+            if not line:
+                warnings.warn("Blank line in sequence data", BiopythonParserWarning)
+                line = self.handle.readline()
+                continue
+            if line == "//":
+                break
+            if line.startswith("CONTIG"):
+                break
+            if len(line) > 9 and line[9:10] != " ":
+                # Some broken programs indent the sequence by one space too many
+                # so try to get rid of that and test again.
+                warnings.warn(
+                    "Invalid indentation for sequence line", BiopythonParserWarning
+                )
+                line = line[1:]
+                if len(line) > 9 and line[9:10] != " ":
+                    raise ValueError(f"Sequence line mal-formed, '{line}'")
+            seq_lines.append(line[10:])  # remove spaces later
+            line = self.handle.readline()
+
+        self.line = line
+        return misc_lines, "".join(seq_lines).replace(" ", "")
+
+    def _feed_first_line(self, consumer, line):
+        """Scan over and parse GenBank LOCUS line (PRIVATE).
+
+        This must cope with several variants, primarily the old and new column
+        based standards from GenBank. Additionally EnsEMBL produces GenBank
+        files where the LOCUS line is space separated rather that following
+        the column based layout.
+
+        We also try to cope with GenBank like files with partial LOCUS lines.
+
+        As of release 229.0, the columns are no longer strictly in a given
+        position. See GenBank format release notes:
+
+            "Historically, the LOCUS line has had a fixed length and its
+            elements have been presented at specific column positions...
+            But with the anticipated increases in the lengths of accession
+            numbers, and the advent of sequences that are gigabases long,
+            maintaining the column positions will not always be possible and
+            the overall length of the LOCUS line could exceed 79 characters."
+
+        """
+        #####################################
+        # LOCUS line                        #
+        #####################################
+        if line[0 : self.GENBANK_INDENT] != "LOCUS       ":
+            raise ValueError("LOCUS line does not start correctly:\n" + line)
+
+        # Have to break up the locus line, and handle the different bits of it.
+        # There are at least two different versions of the locus line...
+        if line[29:33] in [" bp ", " aa ", " rc "] and line[55:62] == "       ":
+            # Old... note we insist on the 55:62 being empty to avoid trying
+            # to parse space separated LOCUS lines from Ensembl etc, see below.
+            #
+            #    Positions  Contents
+            #    ---------  --------
+            #    00:06      LOCUS
+            #    06:12      spaces
+            #    12:??      Locus name
+            #    ??:??      space
+            #    ??:29      Length of sequence, right-justified
+            #    29:33      space, bp, space
+            #    33:41      strand type / molecule type, e.g. DNA
+            #    41:42      space
+            #    42:51      Blank (implies linear), linear or circular
+            #    51:52      space
+            #    52:55      The division code (e.g. BCT, VRL, INV)
+            #    55:62      space
+            #    62:73      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
+            #
+            # assert line[29:33] in [' bp ', ' aa ',' rc '] , \
+            #       'LOCUS line does not contain size units at expected position:\n' + line
+            if line[41:42] != " ":
+                raise ValueError(
+                    "LOCUS line does not contain space at position 42:\n" + line
+                )
+            if line[42:51].strip() not in ["", "linear", "circular"]:
+                raise ValueError(
+                    "LOCUS line does not contain valid entry "
+                    "(linear, circular, ...):\n" + line
+                )
+            if line[51:52] != " ":
+                raise ValueError(
+                    "LOCUS line does not contain space at position 52:\n" + line
+                )
+            # if line[55:62] != '       ':
+            #      raise ValueError('LOCUS line does not contain spaces from position 56 to 62:\n' + line)
+            parse_date = False
+            if line[62:73].strip():
+                parse_date = True
+                if line[64:65] != "-":
+                    parse_date = False
+                    warnings.warn(
+                        "LOCUS line does not contain - "
+                        "at position 65 in date:\n" + line,
+                        BiopythonParserWarning,
+                    )
+                if line[68:69] != "-":
+                    parse_date = False
+                    warnings.warn(
+                        "LOCUS line does not contain - "
+                        "at position 69 in date:\n" + line,
+                        BiopythonParserWarning,
+                    )
+
+            name_and_length_str = line[self.GENBANK_INDENT : 29]
+            while "  " in name_and_length_str:
+                name_and_length_str = name_and_length_str.replace("  ", " ")
+            name_and_length = name_and_length_str.split(" ")
+            if len(name_and_length) > 2:
+                raise ValueError(
+                    "Cannot parse the name and length in the LOCUS line:\n" + line
+                )
+            if len(name_and_length) == 1:
+                raise ValueError("Name and length collide in the LOCUS line:\n" + line)
+            # Should be possible to split them based on position, if
+            # a clear definition of the standard exists THAT AGREES with
+            # existing files.
+            name, length = name_and_length
+            if len(name) > 16:
+                # As long as the sequence is short, can steal its leading spaces
+                # to extend the name over the current 16 character limit.
+                # However, that deserves a warning as it is out of spec.
+                warnings.warn(
+                    "GenBank LOCUS line identifier over 16 characters",
+                    BiopythonParserWarning,
+                )
+            consumer.locus(name)
+            consumer.size(length)
+            # consumer.residue_type(line[33:41].strip())
+
+            if line[33:51].strip() == "" and line[29:33] == " aa ":
+                # Amino acids -> protein (even if there is no residue type given)
+                consumer.residue_type("PROTEIN")
+            else:
+                consumer.residue_type(line[33:51].strip())
+
+            consumer.molecule_type(line[33:41].strip())
+            consumer.topology(line[42:51].strip())
+            consumer.data_file_division(line[52:55])
+            if parse_date:
+                consumer.date(line[62:73])
+        elif line[40:44] in [" bp ", " aa ", " rc "] and line[54:64].strip() in [
+            "",
+            "linear",
+            "circular",
+        ]:
+            # New... linear/circular/big blank test should avoid EnsEMBL style
+            # LOCUS line being treated like a proper column based LOCUS line.
+            #
+            #    Positions  Contents
+            #    ---------  --------
+            #    00:06      LOCUS
+            #    06:12      spaces
+            #    12:??      Locus name
+            #    ??:??      space
+            #    ??:40      Length of sequence, right-justified
+            #    40:44      space, bp, space
+            #    44:47      Blank, ss-, ds-, ms-
+            #    47:54      Blank, DNA, RNA, tRNA, mRNA, uRNA, snRNA, cDNA
+            #    54:55      space
+            #    55:63      Blank (implies linear), linear or circular
+            #    63:64      space
+            #    64:67      The division code (e.g. BCT, VRL, INV)
+            #    67:68      space
+            #    68:79      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
+            #
+            if len(line) < 79:
+                # JBEI genbank files seem to miss a division code and date
+                # See issue #1656 e.g.
+                # LOCUS       pEH010                  5743 bp    DNA     circular
+                warnings.warn(
+                    f"Truncated LOCUS line found - is this correct?\n:{line!r}",
+                    BiopythonParserWarning,
+                )
+                padding_len = 79 - len(line)
+                padding = " " * padding_len
+                line += padding
+
+            if line[40:44] not in [" bp ", " aa ", " rc "]:
+                raise ValueError(
+                    "LOCUS line does not contain size units at "
+                    "expected position:\n" + line
+                )
+            if line[44:47] not in ["   ", "ss-", "ds-", "ms-"]:
+                raise ValueError(
+                    "LOCUS line does not have valid strand "
+                    "type (Single stranded, ...):\n" + line
+                )
+
+            if not (
+                line[47:54].strip() == ""
+                or "DNA" in line[47:54].strip().upper()
+                or "RNA" in line[47:54].strip().upper()
+            ):
+                raise ValueError(
+                    "LOCUS line does not contain valid "
+                    "sequence type (DNA, RNA, ...):\n" + line
+                )
+            if line[54:55] != " ":
+                raise ValueError(
+                    "LOCUS line does not contain space at position 55:\n" + line
+                )
+            if line[55:63].strip() not in ["", "linear", "circular"]:
+                raise ValueError(
+                    "LOCUS line does not contain valid "
+                    "entry (linear, circular, ...):\n" + line
+                )
+            if line[63:64] != " ":
+                raise ValueError(
+                    "LOCUS line does not contain space at position 64:\n" + line
+                )
+            if line[67:68] != " ":
+                raise ValueError(
+                    "LOCUS line does not contain space at position 68:\n" + line
+                )
+            parse_date = False
+            if line[68:79].strip():
+                parse_date = True
+                if line[70:71] != "-":
+                    parse_date = False
+                    warnings.warn(
+                        "LOCUS line does not contain - "
+                        "at position 71 in date:\n" + line,
+                        BiopythonParserWarning,
+                    )
+                if line[74:75] != "-":
+                    parse_date = False
+                    warnings.warn(
+                        "LOCUS line does not contain - "
+                        "at position 75 in date:\n" + line,
+                        BiopythonParserWarning,
+                    )
+
+            name_and_length_str = line[self.GENBANK_INDENT : 40]
+            while "  " in name_and_length_str:
+                name_and_length_str = name_and_length_str.replace("  ", " ")
+            name_and_length = name_and_length_str.split(" ")
+            if len(name_and_length) > 2:
+                raise ValueError(
+                    "Cannot parse the name and length in the LOCUS line:\n" + line
+                )
+            if len(name_and_length) == 1:
+                raise ValueError("Name and length collide in the LOCUS line:\n" + line)
+            # Should be possible to split them based on position, if
+            # a clear definition of the stand exists THAT AGREES with
+            # existing files.
+            consumer.locus(name_and_length[0])
+            consumer.size(name_and_length[1])
+
+            if line[44:54].strip() == "" and line[40:44] == " aa ":
+                # Amino acids -> protein (even if there is no residue type given)
+                consumer.residue_type(("PROTEIN " + line[54:63]).strip())
+            else:
+                consumer.residue_type(line[44:63].strip())
+
+            consumer.molecule_type(line[44:54].strip())
+            consumer.topology(line[55:63].strip())
+            if line[64:76].strip():
+                consumer.data_file_division(line[64:67])
+            if parse_date:
+                consumer.date(line[68:79])
+        elif line[self.GENBANK_INDENT :].strip().count(" ") == 0:
+            # Truncated LOCUS line, as produced by some EMBOSS tools - see bug 1762
+            #
+            # e.g.
+            #
+            #    "LOCUS       U00096"
+            #
+            # rather than:
+            #
+            #    "LOCUS       U00096               4639675 bp    DNA     circular BCT"
+            #
+            #    Positions  Contents
+            #    ---------  --------
+            #    00:06      LOCUS
+            #    06:12      spaces
+            #    12:??      Locus name
+            if line[self.GENBANK_INDENT :].strip() != "":
+                consumer.locus(line[self.GENBANK_INDENT :].strip())
+            else:
+                # Must just have just "LOCUS       ", is this even legitimate?
+                # We should be able to continue parsing... we need real world testcases!
+                warnings.warn(
+                    f"Minimal LOCUS line found - is this correct?\n:{line!r}",
+                    BiopythonParserWarning,
+                )
+        elif (
+            len(line.split()) == 8
+            and line.split()[3] in ("aa", "bp")
+            and line.split()[5] in ("linear", "circular")
+        ):
+            # Cope with invalidly spaced GenBank LOCUS lines like
+            # LOCUS       AB070938          6497 bp    DNA     linear   BCT 11-OCT-2001
+            # This will also cope with extra long accession numbers and
+            # sequence lengths
+            splitline = line.split()
+            consumer.locus(splitline[1])
+            # Provide descriptive error message if the sequence is too long
+            # for python to handle
+
+            if int(splitline[2]) > sys.maxsize:
+                raise ValueError(
+                    "Tried to load a sequence with a length %s, "
+                    "your installation of python can only load "
+                    "sesquences of length %s" % (splitline[2], sys.maxsize)
+                )
+            else:
+                consumer.size(splitline[2])
+
+            consumer.residue_type(splitline[4])
+            consumer.topology(splitline[5])
+            consumer.data_file_division(splitline[6])
+            consumer.date(splitline[7])
+            if len(line) < 80:
+                warnings.warn(
+                    "Attempting to parse malformed locus line:\n%r\n"
+                    "Found locus %r size %r residue_type %r\n"
+                    "Some fields may be wrong."
+                    % (line, splitline[1], splitline[2], splitline[4]),
+                    BiopythonParserWarning,
+                )
+        elif len(line.split()) == 7 and line.split()[3] in ["aa", "bp"]:
+            # Cope with EnsEMBL genbank files which use space separation rather
+            # than the expected column based layout. e.g.
+            # LOCUS       HG531_PATCH 1000000 bp DNA HTG 18-JUN-2011
+            # LOCUS       HG531_PATCH 759984 bp DNA HTG 18-JUN-2011
+            # LOCUS       HG506_HG1000_1_PATCH 814959 bp DNA HTG 18-JUN-2011
+            # LOCUS       HG506_HG1000_1_PATCH 1219964 bp DNA HTG 18-JUN-2011
+            # Notice that the 'bp' can occur in the position expected by either
+            # the old or the new fixed column standards (parsed above).
+            splitline = line.split()
+            consumer.locus(splitline[1])
+            consumer.size(splitline[2])
+            consumer.residue_type(splitline[4])
+            consumer.data_file_division(splitline[5])
+            consumer.date(splitline[6])
+        elif len(line.split()) >= 4 and line.split()[3] in ["aa", "bp"]:
+            # Cope with EMBOSS seqret output where it seems the locus id can cause
+            # the other fields to overflow.  We just IGNORE the other fields!
+            warnings.warn(
+                f"Malformed LOCUS line found - is this correct?\n:{line!r}",
+                BiopythonParserWarning,
+            )
+            consumer.locus(line.split()[1])
+            consumer.size(line.split()[2])
+        elif len(line.split()) >= 4 and line.split()[-1] in ["aa", "bp"]:
+            # Cope with pseudo-GenBank files like this:
+            #   "LOCUS       RNA5 complete       1718 bp"
+            # Treat everything between LOCUS and the size as the identifier.
+            warnings.warn(
+                f"Malformed LOCUS line found - is this correct?\n:{line!r}",
+                BiopythonParserWarning,
+            )
+            consumer.locus(line[5:].rsplit(None, 2)[0].strip())
+            consumer.size(line.split()[-2])
+        else:
+            raise ValueError("Did not recognise the LOCUS line layout:\n" + line)
+
+    def _feed_header_lines(self, consumer, lines):
+        # Following dictionary maps GenBank lines to the associated
+        # consumer methods - the special cases like LOCUS where one
+        # genbank line triggers several consumer calls have to be
+        # handled individually.
+        consumer_dict = {
+            "DEFINITION": "definition",
+            "ACCESSION": "accession",
+            "NID": "nid",
+            "PID": "pid",
+            "DBSOURCE": "db_source",
+            "KEYWORDS": "keywords",
+            "SEGMENT": "segment",
+            "SOURCE": "source",
+            "AUTHORS": "authors",
+            "CONSRTM": "consrtm",
+            "PROJECT": "project",
+            "TITLE": "title",
+            "JOURNAL": "journal",
+            "MEDLINE": "medline_id",
+            "PUBMED": "pubmed_id",
+            "REMARK": "remark",
+        }
+        # We have to handle the following specially:
+        # ORIGIN (locus, size, residue_type, data_file_division and date)
+        # COMMENT (comment)
+        # VERSION (version and gi)
+        # DBLINK (database links like projects, newlines important)
+        # REFERENCE (eference_num and reference_bases)
+        # ORGANISM (organism and taxonomy)
+        lines = [_f for _f in lines if _f]
+        lines.append("")  # helps avoid getting StopIteration all the time
+        line_iter = iter(lines)
+        try:
+            line = next(line_iter)
+            while True:
+                if not line:
+                    break
+                line_type = line[: self.GENBANK_INDENT].strip()
+                data = line[self.GENBANK_INDENT :].strip()
+
+                if line_type == "VERSION":
+                    # Need to call consumer.version(), and maybe also consumer.gi() as well.
+                    # e.g.
+                    # VERSION     AC007323.5  GI:6587720
+                    while "  " in data:
+                        data = data.replace("  ", " ")
+                    if " GI:" not in data:
+                        consumer.version(data)
+                    else:
+                        if self.debug:
+                            print(
+                                "Version ["
+                                + data.split(" GI:")[0]
+                                + "], gi ["
+                                + data.split(" GI:")[1]
+                                + "]"
+                            )
+                        consumer.version(data.split(" GI:")[0])
+                        consumer.gi(data.split(" GI:")[1])
+                    # Read in the next line!
+                    line = next(line_iter)
+                elif line_type == "DBLINK":
+                    # Need to call consumer.dblink() for each line, e.g.
+                    # DBLINK      Project: 57779
+                    #             BioProject: PRJNA57779
+                    line = data.strip()
+                    # Read in the next line, and see if its more of the DBLINK section:
+                    while True:
+                        next_line = next(line_iter)
+                        if next_line[: self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            # No new tag on next line, continue to add dbrefs
+                            if next_line.count(":") == 0:
+                                # This is a continuation of previous dbref
+                                line += " " + next_line.strip()
+                            else:
+                                # Add this continuation to the data string
+                                consumer.dblink(line.strip())
+                                line = next_line
+                            continue
+                        else:
+                            # Add this continuation to the data string
+                            consumer.dblink(line.strip())
+                            # End of the DBLINK, leave this text in the variable "line"
+                            line = next_line
+                            break
+                        line = next(line_iter)
+                elif line_type == "REFERENCE":
+                    if self.debug > 1:
+                        print("Found reference [" + data + "]")
+                    # Need to call consumer.reference_num() and consumer.reference_bases()
+                    # e.g.
+                    # REFERENCE   1  (bases 1 to 86436)
+                    #
+                    # Note that this can be multiline, see Bug 1968, e.g.
+                    #
+                    # REFERENCE   42 (bases 1517 to 1696; 3932 to 4112; 17880 to 17975; 21142 to
+                    #             28259)
+                    #
+                    # For such cases we will call the consumer once only.
+                    data = data.strip()
+
+                    # Read in the next line, and see if its more of the reference:
+                    while True:
+                        line = next(line_iter)
+                        if line[: self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            # Add this continuation to the data string
+                            data += " " + line[self.GENBANK_INDENT :]
+                            if self.debug > 1:
+                                print("Extended reference text [" + data + "]")
+                        else:
+                            # End of the reference, leave this text in the variable "line"
+                            break
+
+                    # We now have all the reference line(s) stored in a string, data,
+                    # which we pass to the consumer
+                    while "  " in data:
+                        data = data.replace("  ", " ")
+                    if " " not in data:
+                        if self.debug > 2:
+                            print('Reference number "' + data + '"')
+                        consumer.reference_num(data)
+                    else:
+                        if self.debug > 2:
+                            print(
+                                'Reference number "'
+                                + data[: data.find(" ")]
+                                + '", "'
+                                + data[data.find(" ") + 1 :]
+                                + '"'
+                            )
+                        consumer.reference_num(data[: data.find(" ")])
+                        consumer.reference_bases(data[data.find(" ") + 1 :])
+                elif line_type == "ORGANISM":
+                    # Typically the first line is the organism, and subsequent lines
+                    # are the taxonomy lineage.  However, given longer and longer
+                    # species names (as more and more strains and sub strains get
+                    # sequenced) the oragnism name can now get wrapped onto multiple
+                    # lines.  The NCBI say we have to recognise the lineage line by
+                    # the presence of semi-colon delimited entries.  In the long term,
+                    # they are considering adding a new keyword (e.g. LINEAGE).
+                    # See Bug 2591 for details.
+                    organism_data = data
+                    lineage_data = ""
+                    while True:
+                        line = next(line_iter)
+                        if line[0 : self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            if (
+                                lineage_data
+                                or ";" in line
+                                or line[self.GENBANK_INDENT :].strip()
+                                in (
+                                    "Bacteria.",
+                                    "Archaea.",
+                                    "Eukaryota.",
+                                    "Unclassified.",
+                                    "Viruses.",
+                                    "cellular organisms.",
+                                    "other sequences.",
+                                    "unclassified sequences.",
+                                )
+                            ):
+                                lineage_data += " " + line[self.GENBANK_INDENT :]
+                            elif line[self.GENBANK_INDENT :].strip() == ".":
+                                # No lineage data, just . place holder
+                                pass
+                            else:
+                                organism_data += (
+                                    " " + line[self.GENBANK_INDENT :].strip()
+                                )
+                        else:
+                            # End of organism and taxonomy
+                            break
+                    consumer.organism(organism_data)
+                    if lineage_data.strip() == "" and self.debug > 1:
+                        print("Taxonomy line(s) missing or blank")
+                    consumer.taxonomy(lineage_data.strip())
+                    del organism_data, lineage_data
+                elif line_type == "COMMENT":
+                    # A COMMENT can either be plain text or tabular (Structured Comment),
+                    # or contain both. Multi-line comments are common. The code calls
+                    # consumer.comment() once with a list where each entry
+                    # is a line. If there's a structured comment consumer.structured_comment()
+                    # is called with a dict of dicts where the secondary key/value pairs are
+                    # the same as those in the structured comment table. The primary key is
+                    # the title or header of the table (e.g. Assembly-Data, FluData). See
+                    # http://www.ncbi.nlm.nih.gov/genbank/structuredcomment
+                    # for more information on Structured Comments.
+                    data = line[self.GENBANK_INDENT :]
+                    if self.debug > 1:
+                        print("Found comment")
+                    comment_list = []
+                    structured_comment_dict = defaultdict(dict)
+                    regex = rf"([^#]+){self.STRUCTURED_COMMENT_START}$"
+                    structured_comment_key = re.search(regex, data)
+                    if structured_comment_key is not None:
+                        structured_comment_key = structured_comment_key.group(1)
+                        if self.debug > 1:
+                            print("Found Structured Comment")
+                    else:
+                        comment_list.append(data)
+
+                    while True:
+                        line = next(line_iter)
+                        data = line[self.GENBANK_INDENT :]
+                        if line[0 : self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            if self.STRUCTURED_COMMENT_START in data:
+                                regex = rf"([^#]+){self.STRUCTURED_COMMENT_START}$"
+                                structured_comment_key = re.search(regex, data)
+                                if structured_comment_key is not None:
+                                    structured_comment_key = (
+                                        structured_comment_key.group(1)
+                                    )
+                                else:
+                                    comment_list.append(data)
+                            elif (
+                                structured_comment_key is not None
+                                and self.STRUCTURED_COMMENT_DELIM.strip() in data
+                            ):
+                                match = re.search(
+                                    rf"(.+?)\s*{self.STRUCTURED_COMMENT_DELIM.strip()}\s*(.*)",
+                                    data,
+                                )
+                                structured_comment_dict[structured_comment_key][
+                                    match.group(1)
+                                ] = match.group(2)
+                                if self.debug > 2:
+                                    print(
+                                        "Structured Comment continuation [" + data + "]"
+                                    )
+                            elif (
+                                structured_comment_key is not None
+                                and self.STRUCTURED_COMMENT_END not in data
+                            ):
+                                # Don't die on a malformed comment, just warn and carry on
+                                if (
+                                    structured_comment_key
+                                    not in structured_comment_dict
+                                ):
+                                    warnings.warn(
+                                        f"Structured comment not parsed on malformed header line: {line}",
+                                        BiopythonParserWarning,
+                                    )
+                                    continue
+
+                                # The current structured comment has a multiline value
+                                previous_value_line = structured_comment_dict[
+                                    structured_comment_key
+                                ][match.group(1)]
+                                structured_comment_dict[structured_comment_key][
+                                    match.group(1)
+                                ] = (previous_value_line + " " + line.strip())
+                            elif self.STRUCTURED_COMMENT_END in data:
+                                # End of structured comment
+                                structured_comment_key = None
+                            else:
+                                comment_list.append(data)
+                                if self.debug > 2:
+                                    print("Comment continuation [" + data + "]")
+                        else:
+                            # End of the comment
+                            break
+                    if comment_list:
+                        consumer.comment(comment_list)
+                    if structured_comment_dict:
+                        consumer.structured_comment(structured_comment_dict)
+                    del comment_list, structured_comment_key, structured_comment_dict
+                elif line_type in consumer_dict:
+                    # It's a semi-automatic entry!
+                    # Now, this may be a multi line entry...
+                    while True:
+                        line = next(line_iter)
+                        if line[0 : self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            data += " " + line[self.GENBANK_INDENT :]
+                        else:
+                            # We now have all the data for this entry:
+
+                            # The DEFINITION field must ends with a period
+                            # # see ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt [3.4.5]
+                            # and discussion https://github.com/biopython/biopython/pull/616
+                            # We consider this period belong to the syntax, not to the data
+                            # So remove it if it exist
+                            if line_type == "DEFINITION" and data.endswith("."):
+                                data = data[:-1]
+                            getattr(consumer, consumer_dict[line_type])(data)
+                            # End of continuation - return to top of loop!
+                            break
+                else:
+                    if self.debug:
+                        print("Ignoring GenBank header line:\n" % line)
+                    # Read in next line
+                    line = next(line_iter)
+        except StopIteration:
+            raise ValueError("Problem in header") from None
+
+    def _feed_misc_lines(self, consumer, lines):
+        # Deals with a few misc lines between the features and the sequence
+        lines.append("")
+        line_iter = iter(lines)
+        try:
+            for line in line_iter:
+                if line.startswith("BASE COUNT"):
+                    line = line[10:].strip()
+                    if line:
+                        if self.debug:
+                            print("base_count = " + line)
+                        consumer.base_count(line)
+                if line.startswith("ORIGIN"):
+                    line = line[6:].strip()
+                    if line:
+                        if self.debug:
+                            print("origin_name = " + line)
+                        consumer.origin_name(line)
+                if line.startswith("TLS "):
+                    line = line[3:].strip()
+                    consumer.tls(line)
+                if line.startswith("TSA "):
+                    line = line[3:].strip()
+                    consumer.tsa(line)
+                if line.startswith("WGS "):
+                    line = line[3:].strip()
+                    consumer.wgs(line)
+                if line.startswith("WGS_SCAFLD"):
+                    line = line[10:].strip()
+                    consumer.add_wgs_scafld(line)
+                if line.startswith("CONTIG"):
+                    line = line[6:].strip()
+                    contig_location = line
+                    while True:
+                        line = next(line_iter)
+                        if not line:
+                            break
+                        elif line[: self.GENBANK_INDENT] == self.GENBANK_SPACER:
+                            # Don't need to preserve the whitespace here.
+                            contig_location += line[self.GENBANK_INDENT :].rstrip()
+                        elif line.startswith("ORIGIN"):
+                            # Strange, seen this in GenPept files via Entrez gbwithparts
+                            line = line[6:].strip()
+                            if line:
+                                consumer.origin_name(line)
+                            break
+                        else:
+                            raise ValueError(
+                                "Expected CONTIG continuation line, got:\n" + line
+                            )
+                    consumer.contig_location(contig_location)
+            return
+        except StopIteration:
+            raise ValueError("Problem in misc lines before sequence") from None

.venv_haddock/lib/python3.12/site-packages/Bio/GenBank/__init__.py

@@ -0,0 +1,1206 @@
+# Copyright 2000 by Jeffrey Chang, Brad Chapman.  All rights reserved.
+# Copyright 2006-2017 by Peter Cock.  All rights reserved.
+#
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code to work with GenBank formatted files.
+
+Rather than using Bio.GenBank, you are now encouraged to use Bio.SeqIO with
+the "genbank" or "embl" format names to parse GenBank or EMBL files into
+SeqRecord and SeqFeature objects (see the Biopython tutorial for details).
+
+Using Bio.GenBank directly to parse GenBank files is only useful if you want
+to obtain GenBank-specific Record objects, which is a much closer
+representation to the raw file contents than the SeqRecord alternative from
+the FeatureParser (used in Bio.SeqIO).
+
+To use the Bio.GenBank parser, there are two helper functions:
+
+    - read                  Parse a handle containing a single GenBank record
+      as Bio.GenBank specific Record objects.
+    - parse                 Iterate over a handle containing multiple GenBank
+      records as Bio.GenBank specific Record objects.
+
+The following internal classes are not intended for direct use and may
+be deprecated in a future release.
+
+Classes:
+ - Iterator              Iterate through a file of GenBank entries
+ - FeatureParser         Parse GenBank data in SeqRecord and SeqFeature objects.
+ - RecordParser          Parse GenBank data into a Record object.
+
+Exceptions:
+ - ParserFailureError    Exception indicating a failure in the parser (ie.
+   scanner or consumer)
+
+"""
+
+import re
+import warnings
+
+from Bio import BiopythonParserWarning
+from Bio.Seq import Seq
+from Bio.SeqFeature import Location
+from Bio.SeqFeature import LocationParserError
+from Bio.SeqFeature import Reference
+from Bio.SeqFeature import SeqFeature
+from Bio.SeqFeature import SimpleLocation
+
+from .Scanner import GenBankScanner
+from .utils import FeatureValueCleaner
+
+# Constants used to parse GenBank header lines
+GENBANK_INDENT = 12
+GENBANK_SPACER = " " * GENBANK_INDENT
+
+# Constants for parsing GenBank feature lines
+FEATURE_KEY_INDENT = 5
+FEATURE_QUALIFIER_INDENT = 21
+FEATURE_KEY_SPACER = " " * FEATURE_KEY_INDENT
+FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT
+
+
+class Iterator:
+    """Iterator interface to move over a file of GenBank entries one at a time (OBSOLETE).
+
+    This class is likely to be deprecated in a future release of Biopython.
+    Please use Bio.SeqIO.parse(..., format="gb") or Bio.GenBank.parse(...)
+    for SeqRecord and GenBank specific Record objects respectively instead.
+    """
+
+    def __init__(self, handle, parser=None):
+        """Initialize the iterator.
+
+        Arguments:
+         - handle - A handle with GenBank entries to iterate through.
+         - parser - An optional parser to pass the entries through before
+           returning them. If None, then the raw entry will be returned.
+
+        """
+        self.handle = handle
+        self._parser = parser
+
+    def __next__(self):
+        """Return the next GenBank record from the handle.
+
+        Will return None if we ran out of records.
+        """
+        if self._parser is None:
+            lines = []
+            while True:
+                line = self.handle.readline()
+                if not line:
+                    return None  # Premature end of file?
+                lines.append(line)
+                if line.rstrip() == "//":
+                    break
+            return "".join(lines)
+        try:
+            return self._parser.parse(self.handle)
+        except StopIteration:
+            return None
+
+    def __iter__(self):
+        """Iterate over the records."""
+        return iter(self.__next__, None)
+
+
+class ParserFailureError(ValueError):
+    """Failure caused by some kind of problem in the parser."""
+
+
+_cleaner = FeatureValueCleaner()
+
+
+class FeatureParser:
+    """Parse GenBank files into Seq + Feature objects (OBSOLETE).
+
+    Direct use of this class is discouraged, and may be deprecated in
+    a future release of Biopython.
+
+    Please use Bio.SeqIO.parse(...) or Bio.SeqIO.read(...) instead.
+    """
+
+    def __init__(self, debug_level=0, use_fuzziness=1, feature_cleaner=None):
+        """Initialize a GenBank parser and Feature consumer.
+
+        Arguments:
+         - debug_level - An optional argument that species the amount of
+           debugging information the parser should spit out. By default we have
+           no debugging info (the fastest way to do things), but if you want
+           you can set this as high as two and see exactly where a parse fails.
+         - use_fuzziness - Specify whether or not to use fuzzy representations.
+           The default is 1 (use fuzziness).
+         - feature_cleaner - A class which will be used to clean out the
+           values of features. This class must implement the function
+           clean_value. GenBank.utils has a "standard" cleaner class, which
+           is used by default.
+
+        """
+        self._scanner = GenBankScanner(debug_level)
+        self.use_fuzziness = use_fuzziness
+        if feature_cleaner:
+            self._cleaner = feature_cleaner
+        else:
+            self._cleaner = _cleaner  # default
+
+    def parse(self, handle):
+        """Parse the specified handle."""
+        _consumer = _FeatureConsumer(self.use_fuzziness, self._cleaner)
+        self._scanner.feed(handle, _consumer)
+        return _consumer.data
+
+
+class RecordParser:
+    """Parse GenBank files into Record objects (OBSOLETE).
+
+    Direct use of this class is discouraged, and may be deprecated in
+    a future release of Biopython.
+
+    Please use the Bio.GenBank.parse(...) or Bio.GenBank.read(...) functions
+    instead.
+    """
+
+    def __init__(self, debug_level=0):
+        """Initialize the parser.
+
+        Arguments:
+         - debug_level - An optional argument that species the amount of
+           debugging information the parser should spit out. By default we have
+           no debugging info (the fastest way to do things), but if you want
+           you can set this as high as two and see exactly where a parse fails.
+
+        """
+        self._scanner = GenBankScanner(debug_level)
+
+    def parse(self, handle):
+        """Parse the specified handle into a GenBank record."""
+        _consumer = _RecordConsumer()
+
+        self._scanner.feed(handle, _consumer)
+        return _consumer.data
+
+
+class _BaseGenBankConsumer:
+    """Abstract GenBank consumer providing useful general functions (PRIVATE).
+
+    This just helps to eliminate some duplication in things that most
+    GenBank consumers want to do.
+    """
+
+    # Special keys in GenBank records that we should remove spaces from
+    # For instance, \translation keys have values which are proteins and
+    # should have spaces and newlines removed from them. This class
+    # attribute gives us more control over specific formatting problems.
+    remove_space_keys = ["translation"]
+
+    def __init__(self):
+        pass
+
+    @staticmethod
+    def _split_keywords(keyword_string):
+        """Split a string of keywords into a nice clean list (PRIVATE)."""
+        # process the keywords into a python list
+        if keyword_string == "" or keyword_string == ".":
+            keywords = ""
+        elif keyword_string[-1] == ".":
+            keywords = keyword_string[:-1]
+        else:
+            keywords = keyword_string
+        keyword_list = keywords.split(";")
+        return [x.strip() for x in keyword_list]
+
+    @staticmethod
+    def _split_accessions(accession_string):
+        """Split a string of accession numbers into a list (PRIVATE)."""
+        # first replace all line feeds with spaces
+        # Also, EMBL style accessions are split with ';'
+        accession = accession_string.replace("\n", " ").replace(";", " ")
+
+        return [x.strip() for x in accession.split() if x.strip()]
+
+    @staticmethod
+    def _split_taxonomy(taxonomy_string):
+        """Split a string with taxonomy info into a list (PRIVATE)."""
+        if not taxonomy_string or taxonomy_string == ".":
+            # Missing data, no taxonomy
+            return []
+
+        if taxonomy_string[-1] == ".":
+            tax_info = taxonomy_string[:-1]
+        else:
+            tax_info = taxonomy_string
+        tax_list = tax_info.split(";")
+        return [
+            item.strip()
+            for tax_item in tax_list
+            for item in tax_item.split("\n")
+            if item
+        ]
+
+    @staticmethod
+    def _clean_location(location_string):
+        """Clean whitespace out of a location string (PRIVATE).
+
+        The location parser isn't a fan of whitespace, so we clean it out
+        before feeding it into the parser.
+        """
+        # Originally this imported string.whitespace and did a replace
+        # via a loop.  It's simpler to just split on whitespace and rejoin
+        # the string - and this avoids importing string too.  See Bug 2684.
+        return "".join(location_string.split())
+
+    @staticmethod
+    def _remove_newlines(text):
+        """Remove any newlines in the passed text, returning the new string (PRIVATE)."""
+        # get rid of newlines in the qualifier value
+        newlines = ["\n", "\r"]
+        for ws in newlines:
+            text = text.replace(ws, "")
+
+        return text
+
+    @staticmethod
+    def _normalize_spaces(text):
+        """Replace multiple spaces in the passed text with single spaces (PRIVATE)."""
+        # get rid of excessive spaces
+        return " ".join(x for x in text.split(" ") if x)
+
+    @staticmethod
+    def _remove_spaces(text):
+        """Remove all spaces from the passed text (PRIVATE)."""
+        return text.replace(" ", "")
+
+    @staticmethod
+    def _convert_to_python_numbers(start, end):
+        """Convert a start and end range to python notation (PRIVATE).
+
+        In GenBank, starts and ends are defined in "biological" coordinates,
+        where 1 is the first base and [i, j] means to include both i and j.
+
+        In python, 0 is the first base and [i, j] means to include i, but
+        not j.
+
+        So, to convert "biological" to python coordinates, we need to
+        subtract 1 from the start, and leave the end and things should
+        be converted happily.
+        """
+        new_start = start - 1
+        new_end = end
+
+        return new_start, new_end
+
+
+class _FeatureConsumer(_BaseGenBankConsumer):
+    """Create a SeqRecord object with Features to return (PRIVATE).
+
+    Attributes:
+     - use_fuzziness - specify whether or not to parse with fuzziness in
+       feature locations.
+     - feature_cleaner - a class that will be used to provide specialized
+       cleaning-up of feature values.
+
+    """
+
+    def __init__(self, use_fuzziness, feature_cleaner=None):
+        from Bio.SeqRecord import SeqRecord
+
+        _BaseGenBankConsumer.__init__(self)
+        self.data = SeqRecord(None, id=None)
+        self.data.id = None
+        self.data.description = ""
+
+        self._use_fuzziness = use_fuzziness
+        self._feature_cleaner = feature_cleaner
+
+        self._seq_type = ""
+        self._seq_data = []
+        self._cur_reference = None
+        self._cur_feature = None
+        self._expected_size = None
+
+    def locus(self, locus_name):
+        """Set the locus name is set as the name of the Sequence."""
+        self.data.name = locus_name
+
+    def size(self, content):
+        """Record the sequence length."""
+        self._expected_size = int(content)
+
+    def residue_type(self, type):
+        """Record the sequence type (SEMI-OBSOLETE).
+
+        This reflects the fact that the topology (linear/circular) and
+        molecule type (e.g. DNA vs RNA) were a single field in early
+        files. Current GenBank/EMBL files have two fields.
+        """
+        self._seq_type = type.strip()
+
+    def topology(self, topology):
+        """Validate and record sequence topology.
+
+        The topology argument should be "linear" or "circular" (string).
+        """
+        if topology:
+            if topology not in ["linear", "circular"]:
+                raise ParserFailureError(
+                    f"Unexpected topology {topology!r} should be linear or circular"
+                )
+            self.data.annotations["topology"] = topology
+
+    def molecule_type(self, mol_type):
+        """Validate and record the molecule type (for round-trip etc)."""
+        if mol_type:
+            if "circular" in mol_type or "linear" in mol_type:
+                raise ParserFailureError(
+                    f"Molecule type {mol_type!r} should not include topology"
+                )
+
+            # Writing out records will fail if we have a lower case DNA
+            # or RNA string in here, so upper case it.
+            # This is a bit ugly, but we don't want to upper case e.g.
+            # the m in mRNA, but thanks to the strip we lost the spaces
+            # so we need to index from the back
+            if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper():
+                warnings.warn(
+                    f"Non-upper case molecule type in LOCUS line: {mol_type}",
+                    BiopythonParserWarning,
+                )
+
+            self.data.annotations["molecule_type"] = mol_type
+
+    def data_file_division(self, division):
+        self.data.annotations["data_file_division"] = division
+
+    def date(self, submit_date):
+        self.data.annotations["date"] = submit_date
+
+    def definition(self, definition):
+        """Set the definition as the description of the sequence."""
+        if self.data.description:
+            # Append to any existing description
+            # e.g. EMBL files with two DE lines.
+            self.data.description += " " + definition
+        else:
+            self.data.description = definition
+
+    def accession(self, acc_num):
+        """Set the accession number as the id of the sequence.
+
+        If we have multiple accession numbers, the first one passed is
+        used.
+        """
+        new_acc_nums = self._split_accessions(acc_num)
+
+        # Also record them ALL in the annotations
+        try:
+            # On the off chance there was more than one accession line:
+            for acc in new_acc_nums:
+                # Prevent repeat entries
+                if acc not in self.data.annotations["accessions"]:
+                    self.data.annotations["accessions"].append(acc)
+        except KeyError:
+            self.data.annotations["accessions"] = new_acc_nums
+
+        # if we haven't set the id information yet, add the first acc num
+        if not self.data.id:
+            if len(new_acc_nums) > 0:
+                # self.data.id = new_acc_nums[0]
+                # Use the FIRST accession as the ID, not the first on this line!
+                self.data.id = self.data.annotations["accessions"][0]
+
+    def tls(self, content):
+        self.data.annotations["tls"] = content.split("-")
+
+    def tsa(self, content):
+        self.data.annotations["tsa"] = content.split("-")
+
+    def wgs(self, content):
+        self.data.annotations["wgs"] = content.split("-")
+
+    def add_wgs_scafld(self, content):
+        self.data.annotations.setdefault("wgs_scafld", []).append(content.split("-"))
+
+    def nid(self, content):
+        self.data.annotations["nid"] = content
+
+    def pid(self, content):
+        self.data.annotations["pid"] = content
+
+    def version(self, version_id):
+        # Want to use the versioned accession as the record.id
+        # This comes from the VERSION line in GenBank files, or the
+        # obsolete SV line in EMBL.  For the new EMBL files we need
+        # both the version suffix from the ID line and the accession
+        # from the AC line.
+        if version_id.count(".") == 1 and version_id.split(".")[1].isdigit():
+            self.accession(version_id.split(".")[0])
+            self.version_suffix(version_id.split(".")[1])
+        elif version_id:
+            # For backwards compatibility...
+            self.data.id = version_id
+
+    def project(self, content):
+        """Handle the information from the PROJECT line as a list of projects.
+
+        e.g.::
+
+            PROJECT     GenomeProject:28471
+
+        or::
+
+            PROJECT     GenomeProject:13543  GenomeProject:99999
+
+        This is stored as dbxrefs in the SeqRecord to be consistent with the
+        projected switch of this line to DBLINK in future GenBank versions.
+        Note the NCBI plan to replace "GenomeProject:28471" with the shorter
+        "Project:28471" as part of this transition.
+        """
+        content = content.replace("GenomeProject:", "Project:")
+        self.data.dbxrefs.extend(p for p in content.split() if p)
+
+    def dblink(self, content):
+        """Store DBLINK cross references as dbxrefs in our record object.
+
+        This line type is expected to replace the PROJECT line in 2009. e.g.
+
+        During transition::
+
+            PROJECT     GenomeProject:28471
+            DBLINK      Project:28471
+                        Trace Assembly Archive:123456
+
+        Once the project line is dropped::
+
+            DBLINK      Project:28471
+                        Trace Assembly Archive:123456
+
+        Note GenomeProject -> Project.
+
+        We'll have to see some real examples to be sure, but based on the
+        above example we can expect one reference per line.
+
+        Note that at some point the NCBI have included an extra space, e.g.::
+
+            DBLINK      Project: 28471
+
+        """
+        # During the transition period with both PROJECT and DBLINK lines,
+        # we don't want to add the same cross reference twice.
+        while ": " in content:
+            content = content.replace(": ", ":")
+        if content.strip() not in self.data.dbxrefs:
+            self.data.dbxrefs.append(content.strip())
+
+    def version_suffix(self, version):
+        """Set the version to overwrite the id.
+
+        Since the version provides the same information as the accession
+        number, plus some extra info, we set this as the id if we have
+        a version.
+        """
+        # e.g. GenBank line:
+        # VERSION     U49845.1  GI:1293613
+        # or the obsolete EMBL line:
+        # SV   U49845.1
+        # Scanner calls consumer.version("U49845.1")
+        # which then calls consumer.version_suffix(1)
+        #
+        # e.g. EMBL new line:
+        # ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
+        # Scanner calls consumer.version_suffix(1)
+        assert version.isdigit()
+        self.data.annotations["sequence_version"] = int(version)
+
+    def db_source(self, content):
+        self.data.annotations["db_source"] = content.rstrip()
+
+    def gi(self, content):
+        self.data.annotations["gi"] = content
+
+    def keywords(self, content):
+        if "keywords" in self.data.annotations:
+            # Multi-line keywords, append to list
+            # Note EMBL states "A keyword is never split between lines."
+            self.data.annotations["keywords"].extend(self._split_keywords(content))
+        else:
+            self.data.annotations["keywords"] = self._split_keywords(content)
+
+    def segment(self, content):
+        self.data.annotations["segment"] = content
+
+    def source(self, content):
+        # Note that some software (e.g. VectorNTI) may produce an empty
+        # source (rather than using a dot/period as might be expected).
+        if content == "":
+            source_info = ""
+        elif content[-1] == ".":
+            source_info = content[:-1]
+        else:
+            source_info = content
+        self.data.annotations["source"] = source_info
+
+    def organism(self, content):
+        self.data.annotations["organism"] = content
+
+    def taxonomy(self, content):
+        """Record (another line of) the taxonomy lineage."""
+        lineage = self._split_taxonomy(content)
+        try:
+            self.data.annotations["taxonomy"].extend(lineage)
+        except KeyError:
+            self.data.annotations["taxonomy"] = lineage
+
+    def reference_num(self, content):
+        """Signal the beginning of a new reference object."""
+        # if we have a current reference that hasn't been added to
+        # the list of references, add it.
+        if self._cur_reference is not None:
+            self.data.annotations["references"].append(self._cur_reference)
+        else:
+            self.data.annotations["references"] = []
+
+        self._cur_reference = Reference()
+
+    def reference_bases(self, content):
+        """Attempt to determine the sequence region the reference entails.
+
+        Possible types of information we may have to deal with:
+
+        (bases 1 to 86436)
+        (sites)
+        (bases 1 to 105654; 110423 to 111122)
+        1  (residues 1 to 182)
+        """
+        # first remove the parentheses
+        assert content.endswith(")"), content
+        ref_base_info = content[1:-1]
+
+        all_locations = []
+        # parse if we've got 'bases' and 'to'
+        if "bases" in ref_base_info and "to" in ref_base_info:
+            # get rid of the beginning 'bases'
+            ref_base_info = ref_base_info[5:]
+            locations = self._split_reference_locations(ref_base_info)
+            all_locations.extend(locations)
+        elif "residues" in ref_base_info and "to" in ref_base_info:
+            residues_start = ref_base_info.find("residues")
+            # get only the information after "residues"
+            ref_base_info = ref_base_info[(residues_start + len("residues ")) :]
+            locations = self._split_reference_locations(ref_base_info)
+            all_locations.extend(locations)
+
+        # make sure if we are not finding information then we have
+        # the string 'sites' or the string 'bases'
+        elif ref_base_info == "sites" or ref_base_info.strip() == "bases":
+            pass
+        # otherwise raise an error
+        else:
+            raise ValueError(
+                f"Could not parse base info {ref_base_info} in record {self.data.id}"
+            )
+
+        self._cur_reference.location = all_locations
+
+    def _split_reference_locations(self, location_string):
+        """Get reference locations out of a string of reference information (PRIVATE).
+
+        The passed string should be of the form::
+
+            1 to 20; 20 to 100
+
+        This splits the information out and returns a list of location objects
+        based on the reference locations.
+        """
+        # split possibly multiple locations using the ';'
+        all_base_info = location_string.split(";")
+
+        new_locations = []
+        for base_info in all_base_info:
+            start, end = base_info.split("to")
+            new_start, new_end = self._convert_to_python_numbers(
+                int(start.strip()), int(end.strip())
+            )
+            this_location = SimpleLocation(new_start, new_end)
+            new_locations.append(this_location)
+        return new_locations
+
+    def authors(self, content):
+        if self._cur_reference.authors:
+            self._cur_reference.authors += " " + content
+        else:
+            self._cur_reference.authors = content
+
+    def consrtm(self, content):
+        if self._cur_reference.consrtm:
+            self._cur_reference.consrtm += " " + content
+        else:
+            self._cur_reference.consrtm = content
+
+    def title(self, content):
+        if self._cur_reference is None:
+            warnings.warn(
+                "GenBank TITLE line without REFERENCE line.", BiopythonParserWarning
+            )
+        elif self._cur_reference.title:
+            self._cur_reference.title += " " + content
+        else:
+            self._cur_reference.title = content
+
+    def journal(self, content):
+        if self._cur_reference.journal:
+            self._cur_reference.journal += " " + content
+        else:
+            self._cur_reference.journal = content
+
+    def medline_id(self, content):
+        self._cur_reference.medline_id = content
+
+    def pubmed_id(self, content):
+        self._cur_reference.pubmed_id = content
+
+    def remark(self, content):
+        """Deal with a reference comment."""
+        if self._cur_reference.comment:
+            self._cur_reference.comment += " " + content
+        else:
+            self._cur_reference.comment = content
+
+    def comment(self, content):
+        try:
+            self.data.annotations["comment"] += "\n" + "\n".join(content)
+        except KeyError:
+            self.data.annotations["comment"] = "\n".join(content)
+
+    def structured_comment(self, content):
+        self.data.annotations["structured_comment"] = content
+
+    def features_line(self, content):
+        """Get ready for the feature table when we reach the FEATURE line."""
+        self.start_feature_table()
+
+    def start_feature_table(self):
+        """Indicate we've got to the start of the feature table."""
+        # make sure we've added on our last reference object
+        if self._cur_reference is not None:
+            self.data.annotations["references"].append(self._cur_reference)
+            self._cur_reference = None
+
+    def feature_key(self, content):
+        # start a new feature
+        self._cur_feature = SeqFeature()
+        self._cur_feature.type = content
+        self.data.features.append(self._cur_feature)
+
+    def location(self, content):
+        """Parse out location information from the location string.
+
+        This uses simple Python code with some regular expressions to do the
+        parsing, and then translates the results into appropriate objects.
+        """
+        # clean up newlines and other whitespace inside the location before
+        # parsing - locations should have no whitespace whatsoever
+        location_line = self._clean_location(content)
+
+        # Older records have junk like replace(266,"c") in the
+        # location line. Newer records just replace this with
+        # the number 266 and have the information in a more reasonable
+        # place. So we'll just grab out the number and feed this to the
+        # parser. We shouldn't really be losing any info this way.
+        if "replace" in location_line:
+            comma_pos = location_line.find(",")
+            location_line = location_line[8:comma_pos]
+
+        length = self._expected_size
+        # Check if the sequence is circular for features that span the origin
+        is_circular = "circular" in self.data.annotations.get("topology", "").lower()
+        stranded = "PROTEIN" not in self._seq_type.upper()
+
+        try:
+            location = Location.fromstring(location_line, length, is_circular, stranded)
+        except LocationParserError as e:
+            warnings.warn(
+                f"{e}; setting feature location to None.", BiopythonParserWarning
+            )
+            location = None
+        self._cur_feature.location = location
+
+    def feature_qualifier(self, key, value):
+        """When we get a qualifier key and its value.
+
+        Can receive None, since you can have valueless keys such as /pseudo
+        """
+        # Hack to try to preserve historical behaviour of /pseudo etc
+        if value is None:
+            # if the key doesn't exist yet, add an empty string
+            if key not in self._cur_feature.qualifiers:
+                self._cur_feature.qualifiers[key] = [""]
+                return
+            # otherwise just skip this key
+            return
+
+        # Remove enclosing quotation marks
+        if len(value) > 1 and value[0] == '"' and value[-1] == '"':
+            value = value[1:-1]
+
+        # Handle NCBI escaping
+        # Warn if escaping is not according to standard
+        if re.search(r'[^"]"[^"]|^"[^"]|[^"]"$', value):
+            warnings.warn(
+                'The NCBI states double-quote characters like " should be escaped as "" '
+                "(two double - quotes), but here it was not: %r" % value,
+                BiopythonParserWarning,
+            )
+        # Undo escaping, repeated double quotes -> one double quote
+        value = value.replace('""', '"')
+
+        if self._feature_cleaner is not None:
+            value = self._feature_cleaner.clean_value(key, value)
+
+        # if the qualifier name exists, append the value
+        if key in self._cur_feature.qualifiers:
+            self._cur_feature.qualifiers[key].append(value)
+        # otherwise start a new list of the key with its values
+        else:
+            self._cur_feature.qualifiers[key] = [value]
+
+    def feature_qualifier_name(self, content_list):
+        """Use feature_qualifier instead (OBSOLETE)."""
+        raise NotImplementedError("Use the feature_qualifier method instead.")
+
+    def feature_qualifier_description(self, content):
+        """Use feature_qualifier instead (OBSOLETE)."""
+        raise NotImplementedError("Use the feature_qualifier method instead.")
+
+    def contig_location(self, content):
+        """Deal with CONTIG information."""
+        # Historically this was stored as a SeqFeature object, but it was
+        # stored under record.annotations["contig"] and not under
+        # record.features with the other SeqFeature objects.
+        #
+        # The CONTIG location line can include additional tokens like
+        # Gap(), Gap(100) or Gap(unk100) which are not used in the feature
+        # location lines, so storing it using SeqFeature based location
+        # objects is difficult.
+        #
+        # We now store this a string, which means for BioSQL we are now in
+        # much better agreement with how BioPerl records the CONTIG line
+        # in the database.
+        #
+        # NOTE - This code assumes the scanner will return all the CONTIG
+        # lines already combined into one long string!
+        self.data.annotations["contig"] = content
+
+    def origin_name(self, content):
+        pass
+
+    def base_count(self, content):
+        pass
+
+    def base_number(self, content):
+        pass
+
+    def sequence(self, content):
+        """Add up sequence information as we get it.
+
+        To try and make things speedier, this puts all of the strings
+        into a list of strings, and then uses string.join later to put
+        them together. Supposedly, this is a big time savings
+        """
+        assert " " not in content
+        self._seq_data.append(content.upper())
+
+    def record_end(self, content):
+        """Clean up when we've finished the record."""
+        # Try and append the version number to the accession for the full id
+        if not self.data.id:
+            if "accessions" in self.data.annotations:
+                raise ValueError(
+                    "Problem adding version number to accession: "
+                    + str(self.data.annotations["accessions"])
+                )
+            self.data.id = self.data.name  # Good fall back?
+        elif self.data.id.count(".") == 0:
+            try:
+                self.data.id += ".%i" % self.data.annotations["sequence_version"]
+            except KeyError:
+                pass
+
+        # add the sequence information
+
+        sequence = "".join(self._seq_data)
+
+        if (
+            self._expected_size is not None
+            and len(sequence) != 0
+            and self._expected_size != len(sequence)
+        ):
+            warnings.warn(
+                "Expected sequence length %i, found %i (%s)."
+                % (self._expected_size, len(sequence), self.data.id),
+                BiopythonParserWarning,
+            )
+
+        molecule_type = None
+        if self._seq_type:
+            # mRNA is really also DNA, since it is actually cDNA
+            if "DNA" in self._seq_type.upper() or "MRNA" in self._seq_type.upper():
+                molecule_type = "DNA"
+            # are there ever really RNA sequences in GenBank?
+            elif "RNA" in self._seq_type.upper():
+                # Even for data which was from RNA, the sequence string
+                # is usually given as DNA (T not U).  Bug 3010
+                molecule_type = "RNA"
+            elif (
+                "PROTEIN" in self._seq_type.upper() or self._seq_type == "PRT"
+            ):  # PRT is used in EMBL-bank for patents
+                molecule_type = "protein"
+            # work around ugly GenBank records which have circular or
+            # linear but no indication of sequence type
+            elif self._seq_type in ["circular", "linear", "unspecified"]:
+                pass
+            # we have a bug if we get here
+            else:
+                raise ValueError(
+                    f"Could not determine molecule_type for seq_type {self._seq_type}"
+                )
+        # Don't overwrite molecule_type
+        if molecule_type is not None:
+            self.data.annotations["molecule_type"] = self.data.annotations.get(
+                "molecule_type", molecule_type
+            )
+        if not sequence and self._expected_size:
+            self.data.seq = Seq(None, length=self._expected_size)
+        else:
+            self.data.seq = Seq(sequence)
+
+
+class _RecordConsumer(_BaseGenBankConsumer):
+    """Create a GenBank Record object from scanner generated information (PRIVATE)."""
+
+    def __init__(self):
+        _BaseGenBankConsumer.__init__(self)
+        from . import Record
+
+        self.data = Record.Record()
+
+        self._seq_data = []
+        self._cur_reference = None
+        self._cur_feature = None
+        self._cur_qualifier = None
+
+    def tls(self, content):
+        self.data.tls = content.split("-")
+
+    def tsa(self, content):
+        self.data.tsa = content.split("-")
+
+    def wgs(self, content):
+        self.data.wgs = content.split("-")
+
+    def add_wgs_scafld(self, content):
+        self.data.wgs_scafld.append(content.split("-"))
+
+    def locus(self, content):
+        self.data.locus = content
+
+    def size(self, content):
+        self.data.size = content
+
+    def residue_type(self, content):
+        # Be lenient about parsing, but technically lowercase residue types are malformed.
+        if "dna" in content or "rna" in content:
+            warnings.warn(
+                f"Invalid seq_type ({content}): DNA/RNA should be uppercase.",
+                BiopythonParserWarning,
+            )
+        self.data.residue_type = content
+
+    def data_file_division(self, content):
+        self.data.data_file_division = content
+
+    def date(self, content):
+        self.data.date = content
+
+    def definition(self, content):
+        self.data.definition = content
+
+    def accession(self, content):
+        for acc in self._split_accessions(content):
+            if acc not in self.data.accession:
+                self.data.accession.append(acc)
+
+    def molecule_type(self, mol_type):
+        """Validate and record the molecule type (for round-trip etc)."""
+        if mol_type:
+            if "circular" in mol_type or "linear" in mol_type:
+                raise ParserFailureError(
+                    f"Molecule type {mol_type!r} should not include topology"
+                )
+
+            # Writing out records will fail if we have a lower case DNA
+            # or RNA string in here, so upper case it.
+            # This is a bit ugly, but we don't want to upper case e.g.
+            # the m in mRNA, but thanks to the strip we lost the spaces
+            # so we need to index from the back
+            if mol_type[-3:].upper() in ("DNA", "RNA") and not mol_type[-3:].isupper():
+                warnings.warn(
+                    f"Non-upper case molecule type in LOCUS line: {mol_type}",
+                    BiopythonParserWarning,
+                )
+
+            self.data.molecule_type = mol_type
+
+    def topology(self, topology):
+        """Validate and record sequence topology.
+
+        The topology argument should be "linear" or "circular" (string).
+        """
+        if topology:
+            if topology not in ["linear", "circular"]:
+                raise ParserFailureError(
+                    f"Unexpected topology {topology!r} should be linear or circular"
+                )
+            self.data.topology = topology
+
+    def nid(self, content):
+        self.data.nid = content
+
+    def pid(self, content):
+        self.data.pid = content
+
+    def version(self, content):
+        self.data.version = content
+
+    def db_source(self, content):
+        self.data.db_source = content.rstrip()
+
+    def gi(self, content):
+        self.data.gi = content
+
+    def keywords(self, content):
+        self.data.keywords = self._split_keywords(content)
+
+    def project(self, content):
+        self.data.projects.extend(p for p in content.split() if p)
+
+    def dblink(self, content):
+        self.data.dblinks.append(content)
+
+    def segment(self, content):
+        self.data.segment = content
+
+    def source(self, content):
+        self.data.source = content
+
+    def organism(self, content):
+        self.data.organism = content
+
+    def taxonomy(self, content):
+        self.data.taxonomy = self._split_taxonomy(content)
+
+    def reference_num(self, content):
+        """Grab the reference number and signal the start of a new reference."""
+        # check if we have a reference to add
+        if self._cur_reference is not None:
+            self.data.references.append(self._cur_reference)
+
+        from . import Record
+
+        self._cur_reference = Record.Reference()
+        self._cur_reference.number = content
+
+    def reference_bases(self, content):
+        self._cur_reference.bases = content
+
+    def authors(self, content):
+        self._cur_reference.authors = content
+
+    def consrtm(self, content):
+        self._cur_reference.consrtm = content
+
+    def title(self, content):
+        if self._cur_reference is None:
+            warnings.warn(
+                "GenBank TITLE line without REFERENCE line.", BiopythonParserWarning
+            )
+            return
+        self._cur_reference.title = content
+
+    def journal(self, content):
+        self._cur_reference.journal = content
+
+    def medline_id(self, content):
+        self._cur_reference.medline_id = content
+
+    def pubmed_id(self, content):
+        self._cur_reference.pubmed_id = content
+
+    def remark(self, content):
+        self._cur_reference.remark = content
+
+    def comment(self, content):
+        self.data.comment += "\n".join(content)
+
+    def structured_comment(self, content):
+        self.data.structured_comment = content
+
+    def primary_ref_line(self, content):
+        """Save reference data for the PRIMARY line."""
+        self.data.primary.append(content)
+
+    def primary(self, content):
+        pass
+
+    def features_line(self, content):
+        """Get ready for the feature table when we reach the FEATURE line."""
+        self.start_feature_table()
+
+    def start_feature_table(self):
+        """Signal the start of the feature table."""
+        # we need to add on the last reference
+        if self._cur_reference is not None:
+            self.data.references.append(self._cur_reference)
+
+    def feature_key(self, content):
+        """Grab the key of the feature and signal the start of a new feature."""
+        # first add on feature information if we've got any
+        self._add_feature()
+
+        from . import Record
+
+        self._cur_feature = Record.Feature()
+        self._cur_feature.key = content
+
+    def _add_feature(self):
+        """Add a feature to the record, with relevant checks (PRIVATE).
+
+        This does all of the appropriate checking to make sure we haven't
+        left any info behind, and that we are only adding info if it
+        exists.
+        """
+        if self._cur_feature is not None:
+            # if we have a left over qualifier, add it to the qualifiers
+            # on the current feature
+            if self._cur_qualifier is not None:
+                self._cur_feature.qualifiers.append(self._cur_qualifier)
+
+            self._cur_qualifier = None
+            self.data.features.append(self._cur_feature)
+
+    def location(self, content):
+        self._cur_feature.location = self._clean_location(content)
+
+    def feature_qualifier(self, key, value):
+        self.feature_qualifier_name([key])
+        if value is not None:
+            self.feature_qualifier_description(value)
+
+    def feature_qualifier_name(self, content_list):
+        """Deal with qualifier names.
+
+        We receive a list of keys, since you can have valueless keys such as
+        /pseudo which would be passed in with the next key (since no other
+        tags separate them in the file)
+        """
+        from . import Record
+
+        for content in content_list:
+            # the record parser keeps the /s -- add them if we don't have 'em
+            if not content.startswith("/"):
+                content = f"/{content}"
+            # add on a qualifier if we've got one
+            if self._cur_qualifier is not None:
+                self._cur_feature.qualifiers.append(self._cur_qualifier)
+
+            self._cur_qualifier = Record.Qualifier()
+            self._cur_qualifier.key = content
+
+    def feature_qualifier_description(self, content):
+        # if we have info then the qualifier key should have a ='s
+        if "=" not in self._cur_qualifier.key:
+            self._cur_qualifier.key = f"{self._cur_qualifier.key}="
+        cur_content = self._remove_newlines(content)
+        # remove all spaces from the value if it is a type where spaces
+        # are not important
+        for remove_space_key in self.__class__.remove_space_keys:
+            if remove_space_key in self._cur_qualifier.key:
+                cur_content = self._remove_spaces(cur_content)
+        self._cur_qualifier.value = self._normalize_spaces(cur_content)
+
+    def base_count(self, content):
+        self.data.base_counts = content
+
+    def origin_name(self, content):
+        self.data.origin = content
+
+    def contig_location(self, content):
+        """Signal that we have contig information to add to the record."""
+        self.data.contig = self._clean_location(content)
+
+    def sequence(self, content):
+        """Add sequence information to a list of sequence strings.
+
+        This removes spaces in the data and uppercases the sequence, and
+        then adds it to a list of sequences. Later on we'll join this
+        list together to make the final sequence. This is faster than
+        adding on the new string every time.
+        """
+        assert " " not in content
+        self._seq_data.append(content.upper())
+
+    def record_end(self, content):
+        """Signal the end of the record and do any necessary clean-up."""
+        # add together all of the sequence parts to create the
+        # final sequence string
+        self.data.sequence = "".join(self._seq_data)
+        # add on the last feature
+        self._add_feature()
+
+
+def parse(handle):
+    """Iterate over GenBank formatted entries as Record objects.
+
+    >>> from Bio import GenBank
+    >>> with open("GenBank/NC_000932.gb") as handle:
+    ...     for record in GenBank.parse(handle):
+    ...         print(record.accession)
+    ['NC_000932']
+
+    To get SeqRecord objects use Bio.SeqIO.parse(..., format="gb")
+    instead.
+    """
+    return iter(Iterator(handle, RecordParser()))
+
+
+def read(handle):
+    """Read a handle containing a single GenBank entry as a Record object.
+
+    >>> from Bio import GenBank
+    >>> with open("GenBank/NC_000932.gb") as handle:
+    ...     record = GenBank.read(handle)
+    ...     print(record.accession)
+    ['NC_000932']
+
+    To get a SeqRecord object use Bio.SeqIO.read(..., format="gb")
+    instead.
+    """
+    iterator = parse(handle)
+    try:
+        record = next(iterator)
+    except StopIteration:
+        raise ValueError("No records found in handle") from None
+    try:
+        next(iterator)
+        raise ValueError("More than one record found in handle")
+    except StopIteration:
+        pass
+    return record
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/GenBank/utils.py

@@ -0,0 +1,66 @@
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+#
+
+"""Useful utilities for helping in parsing GenBank files."""
+
+
+class FeatureValueCleaner:
+    r"""Provide specialized capabilities for cleaning up values in features.
+
+    This class is designed to provide a mechanism to clean up and process
+    values in the key/value pairs of GenBank features. This is useful
+    because in cases like::
+
+         /translation="MED
+         YDPWNLRFQSKYKSRDA"
+
+    you'll otherwise end up with white space in it.
+
+    This cleaning needs to be done on a case by case basis since it is
+    impossible to interpret whether you should be concatenating everything
+    (as in translations), or combining things with spaces (as might be
+    the case with /notes).
+
+    >>> cleaner = FeatureValueCleaner(["translation"])
+    >>> cleaner
+    FeatureValueCleaner(['translation'])
+    >>> cleaner.clean_value("translation", "MED\nYDPWNLRFQSKYKSRDA")
+    'MEDYDPWNLRFQSKYKSRDA'
+    """
+
+    keys_to_process = ["translation"]
+
+    def __init__(self, to_process=keys_to_process):
+        """Initialize with the keys we should deal with."""
+        self._to_process = to_process
+
+    def __repr__(self):
+        """Return a string representation of the class."""
+        return f"{self.__class__.__name__}({self._to_process!r})"
+
+    def clean_value(self, key_name, value):
+        """Clean the specified value and return it.
+
+        If the value is not specified to be dealt with, the original value
+        will be returned.
+        """
+        if key_name in self._to_process:
+            try:
+                cleaner = getattr(self, f"_clean_{key_name}")
+            except AttributeError:
+                raise AssertionError(f"No function to clean key: {key_name}") from None
+            value = cleaner(value)
+        return value
+
+    def _clean_translation(self, value):
+        """Concatenate a translation value to one long protein string (PRIVATE)."""
+        translation_parts = value.split()
+        return "".join(translation_parts)
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/Geo/Record.py

@@ -0,0 +1,90 @@
+# Copyright 2001 by Katharine Lindner.  All rights reserved.
+# Copyright 2006 by PeterC.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Hold GEO data in a straightforward format.
+
+classes:
+o Record - All of the information in an GEO record.
+
+See http://www.ncbi.nlm.nih.gov/geo/
+"""
+
+
+class Record:
+    """Hold GEO information in a format similar to the original record.
+
+    The Record class is meant to make data easy to get to when you are
+    just interested in looking at GEO data.
+
+    Attributes:
+    entity_type
+    entity_id
+    entity_attributes
+    col_defs
+    table_rows
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.entity_type = ""
+        self.entity_id = ""
+        self.entity_attributes = {}
+        self.col_defs = {}
+        self.table_rows = []
+
+    def __str__(self):
+        """Return the GEO record as a string."""
+        output = ""
+        output += f"GEO Type: {self.entity_type}\n"
+        output += f"GEO Id: {self.entity_id}\n"
+        att_keys = sorted(self.entity_attributes)
+        for key in att_keys:
+            contents = self.entity_attributes[key]
+            if isinstance(contents, list):
+                for item in contents:
+                    try:
+                        output += f"{key}: {item[:40]}\n"
+                        output += out_block(item[40:])
+                    except Exception:  # TODO: IndexError?
+                        pass
+            elif isinstance(contents, str):
+                output += f"{key}: {contents[:40]}\n"
+                output += out_block(contents[40:])
+            else:
+                raise RuntimeError(f"unexpected contents of type {type(contents)}")
+        col_keys = sorted(self.col_defs)
+        output += "Column Header Definitions\n"
+        for key in col_keys:
+            val = self.col_defs[key]
+            output += f"    {key}: {val[:40]}\n"
+            output += out_block(val[40:], "    ")
+        # May have to display VERY large tables,
+        # so only show the first 20 lines of data
+        MAX_ROWS = 20 + 1  # include header in count
+        for row in self.table_rows[0:MAX_ROWS]:
+            output += f"{self.table_rows.index(row)}: "
+            for col in row:
+                output += f"{col}\t"
+            output += "\n"
+        if len(self.table_rows) > MAX_ROWS:
+            output += "...\n"
+            row = self.table_rows[-1]
+            output += f"{self.table_rows.index(row)}: "
+            for col in row:
+                output += f"{col}\t"
+            output += "\n"
+
+        return output
+
+
+def out_block(text, prefix=""):
+    """Format text in blocks of 80 chars with an additional optional prefix."""
+    output = ""
+    for j in range(0, len(text), 80):
+        output += f"{prefix}{text[j : j + 80]}\n"
+    output += "\n"
+    return output