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| """Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format. |
| |
| You are expected to use this module via the Bio.SeqIO functions. |
| See also the Bio.SwissProt module which offers more than just accessing |
| the sequences as SeqRecord objects. |
| |
| See also Bio.SeqIO.UniprotIO.py which supports the "uniprot-xml" format. |
| """ |
|
|
| from Bio import SeqFeature |
| from Bio import SwissProt |
| from Bio.Seq import Seq |
| from Bio.SeqRecord import SeqRecord |
|
|
| from .Interfaces import _TextIOSource |
| from .Interfaces import SequenceIterator |
|
|
|
|
| class SwissIterator(SequenceIterator): |
| """Parser to break up a Swiss-Prot/UniProt file into SeqRecord objects.""" |
|
|
| modes = "t" |
|
|
| def __init__(self, source: _TextIOSource) -> None: |
| """Iterate over a Swiss-Prot file and return SeqRecord objects. |
| |
| Arguments: |
| - source - input stream opened in text mode, or a path to a file |
| |
| Every section from the ID line to the terminating // becomes |
| a single SeqRecord with associated annotation and features. |
| |
| This parser is for the flat file "swiss" format as used by: |
| - Swiss-Prot aka SwissProt |
| - TrEMBL |
| - UniProtKB aka UniProt Knowledgebase |
| |
| For consistency with BioPerl and EMBOSS we call this the "swiss" |
| format. See also the SeqIO support for "uniprot-xml" format. |
| |
| Rather than calling it directly, you are expected to use this |
| parser via Bio.SeqIO.parse(..., format="swiss") instead. |
| """ |
| super().__init__(source, fmt="SwissProt") |
|
|
| def __next__(self): |
| swiss_record = SwissProt._read(self.stream) |
| if swiss_record is None: |
| raise StopIteration |
| |
| record = SeqRecord( |
| Seq(swiss_record.sequence), |
| id=swiss_record.accessions[0], |
| name=swiss_record.entry_name, |
| description=swiss_record.description, |
| features=swiss_record.features, |
| ) |
| for cross_reference in swiss_record.cross_references: |
| if len(cross_reference) < 2: |
| continue |
| database, accession = cross_reference[:2] |
| dbxref = f"{database}:{accession}" |
| if dbxref not in record.dbxrefs: |
| record.dbxrefs.append(dbxref) |
| annotations = record.annotations |
| annotations["molecule_type"] = "protein" |
| annotations["accessions"] = swiss_record.accessions |
| if swiss_record.protein_existence: |
| annotations["protein_existence"] = swiss_record.protein_existence |
| if swiss_record.created: |
| date, version = swiss_record.created |
| annotations["date"] = date |
| annotations["sequence_version"] = version |
| if swiss_record.sequence_update: |
| date, version = swiss_record.sequence_update |
| annotations["date_last_sequence_update"] = date |
| annotations["sequence_version"] = version |
| if swiss_record.annotation_update: |
| date, version = swiss_record.annotation_update |
| annotations["date_last_annotation_update"] = date |
| annotations["entry_version"] = version |
| if swiss_record.gene_name: |
| annotations["gene_name"] = swiss_record.gene_name |
| annotations["organism"] = swiss_record.organism.rstrip(".") |
| annotations["taxonomy"] = swiss_record.organism_classification |
| annotations["ncbi_taxid"] = swiss_record.taxonomy_id |
| if swiss_record.host_organism: |
| annotations["organism_host"] = swiss_record.host_organism |
| if swiss_record.host_taxonomy_id: |
| annotations["host_ncbi_taxid"] = swiss_record.host_taxonomy_id |
| if swiss_record.comments: |
| annotations["comment"] = "\n".join(swiss_record.comments) |
| if swiss_record.references: |
| annotations["references"] = [] |
| for reference in swiss_record.references: |
| feature = SeqFeature.Reference() |
| feature.comment = " ".join("%s=%s;" % k_v for k_v in reference.comments) |
| for key, value in reference.references: |
| if key == "PubMed": |
| feature.pubmed_id = value |
| elif key == "MEDLINE": |
| feature.medline_id = value |
| elif key == "DOI": |
| pass |
| elif key == "AGRICOLA": |
| pass |
| else: |
| raise ValueError(f"Unknown key {key} found in references") |
| feature.authors = reference.authors |
| feature.title = reference.title |
| feature.journal = reference.location |
| annotations["references"].append(feature) |
| if swiss_record.keywords: |
| record.annotations["keywords"] = swiss_record.keywords |
| return record |
|
|
