idx int64 0 251k | question stringlengths 53 3.53k | target stringlengths 5 1.23k | len_question int64 20 893 | len_target int64 3 238 |
|---|---|---|---|---|
15,700 | def move_file_to_file ( old_path , new_path ) : try : os . rename ( old_path , new_path ) except : old_file = os . path . basename ( old_path ) target_directory , target_file = os . path . dirname ( os . path . abspath ( new_path ) ) , os . path . basename ( new_path ) Document . move_file_to_directory ( old_path , target_directory ) # move old file to new directory, change name to new name os . rename ( os . path . join ( target_directory , old_file ) , os . path . join ( target_directory , target_file ) ) | Moves file from old location to new one | 153 | 9 |
15,701 | def write_data ( self , data ) : with open ( self . path , "w" ) as writer : writer . write ( data ) | Writes given data to given path file | 30 | 8 |
15,702 | def get_path_name ( self ) : path = fix_raw_path ( os . path . dirname ( os . path . abspath ( self . path ) ) ) name = os . path . basename ( self . path ) return path , name | Gets path and name of song | 55 | 7 |
15,703 | def get_path_name ( self ) : complete_path = os . path . dirname ( os . path . abspath ( self . path ) ) name = self . path . replace ( complete_path + PATH_SEPARATOR , "" ) if name . endswith ( "/" ) : name = name [ : - 1 ] return complete_path , name | Gets path and name of file | 78 | 7 |
15,704 | def save ( self , page , language , data , change , extra_data = None ) : # if this placeholder is untranslated, we save everything # in the default language if self . untranslated : language = settings . PAGE_DEFAULT_LANGUAGE # the page is being changed if change : # we need create a new content if revision is enabled if ( settings . PAGE_CONTENT_REVISION and self . name not in settings . PAGE_CONTENT_REVISION_EXCLUDE_LIST ) : Content . objects . create_content_if_changed ( page , language , self . name , data ) else : Content . objects . set_or_create_content ( page , language , self . name , data ) # the page is being added else : Content . objects . set_or_create_content ( page , language , self . name , data ) | Actually save the placeholder data into the Content object . | 190 | 10 |
15,705 | def render ( self , context ) : content = mark_safe ( self . get_content_from_context ( context ) ) if not content : return '' if self . parsed : try : t = template . Template ( content , name = self . name ) content = mark_safe ( t . render ( context ) ) except TemplateSyntaxError as error : if global_settings . DEBUG : content = PLACEHOLDER_ERROR % { 'name' : self . name , 'error' : error , } else : content = '' if self . as_varname is None : return content context [ self . as_varname ] = content return '' | Output the content of the PlaceholdeNode in the template . | 140 | 13 |
15,706 | def from_string ( cls , action_str ) : args = { } try : mod_obj = ast . parse ( action_str ) except ( SyntaxError , ValueError ) as e : raise e else : call_obj = mod_obj . body [ 0 ] . value if isinstance ( call_obj , ast . Attribute ) : # Seems like we have a simple function name # (for example `module.function`) module = call_obj . value . id func = call_obj . attr elif isinstance ( call_obj , ast . Call ) : # Seems like we have a function call, maybe with # a few parameters. # Note that we only support `module.function()` format. # You can't use `function()`. try : module = call_obj . func . value . id func = call_obj . func . attr except AttributeError : raise UnsupportedActionError ( action_str ) else : # If we have arguments, they MUST be named: for kwarg in call_obj . keywords : # We only support Strings and Numerics: if isinstance ( kwarg . value , ast . Num ) : args . update ( { kwarg . arg : kwarg . value . n } ) elif isinstance ( kwarg . value , ast . Str ) : args . update ( { kwarg . arg : kwarg . value . s } ) else : raise UnsupportedActionArgumentError ( action_str , kwarg ) else : raise UnsupportedActionError ( action_str ) return cls ( module , func , args ) | Creates a new Action instance from the given string . | 348 | 11 |
15,707 | def sanitize ( self , content ) : import html5lib from html5lib import sanitizer p = html5lib . HTMLParser ( tokenizer = sanitizer . HTMLSanitizer ) dom_tree = p . parseFragment ( content ) return dom_tree . text | Sanitize a string in order to avoid possible XSS using html5lib . | 61 | 17 |
15,708 | def consume ( self , cwd = None ) : first_pass = Grammar . overall . parseString ( self . string ) lowered = { key . lower ( ) : val for key , val in first_pass . iteritems ( ) } self . commands = [ '\n' . join ( self . _get ( 'commands' , lowered ) ) ] self . job_options = self . _get ( 'job_options' , lowered ) self . global_options = self . _get ( 'options' , lowered ) self . files = self . _get ( 'files' , lowered ) self . paths = self . _get ( 'paths' , lowered ) self . files = self . _parse ( self . files , Grammar . file , True ) self . paths = self . _parse ( self . paths , Grammar . path , True ) self . job_options = self . _parse ( self . job_options , Grammar . line ) try : command_lines = self . _parse ( self . commands , Grammar . command_lines ) [ 0 ] except IndexError : raise ValueError ( 'Did you write any commands?' ) self . commands = [ ] for command_line in command_lines : comments , command = command_line self . commands . append ( [ comments . asList ( ) , self . _parse ( [ '' . join ( command ) ] , Grammar . command ) ] ) self . job_options = [ opt . asList ( ) for opt in self . job_options ] self . paths = ctf . get_paths ( self . paths ) self . files = ctf . get_files ( self . files ) self . paths . reverse ( ) self . files . reverse ( ) self . commands . reverse ( ) return ctf . get_command_templates ( self . commands , self . files [ : ] , self . paths [ : ] , self . job_options ) | Converts the lexer tokens into valid statements . This process also checks command syntax . | 413 | 17 |
15,709 | def _get ( self , key , parser_result ) : try : list_data = parser_result [ key ] . asList ( ) if any ( isinstance ( obj , str ) for obj in list_data ) : txt_lines = [ '' . join ( list_data ) ] else : txt_lines = [ '' . join ( f ) for f in list_data ] except KeyError : txt_lines = [ ] return txt_lines | Given a type and a dict of parser results return the items as a list . | 100 | 16 |
15,710 | def _parse ( self , lines , grammar , ignore_comments = False ) : results = [ ] for c in lines : if c != '' and not ( ignore_comments and c [ 0 ] == '#' ) : try : results . append ( grammar . parseString ( c ) ) except pyparsing . ParseException as e : raise ValueError ( 'Invalid syntax. Verify line {} is ' 'correct.\n{}\n\n{}' . format ( e . lineno , c , e ) ) return results | Given a type and a list parse it using the more detailed parse grammar . | 114 | 15 |
15,711 | def objectprep ( self ) : # Move the files to subfolders and create objects self . runmetadata = createobject . ObjectCreation ( self ) if self . extension == 'fastq' : # To streamline the CLARK process, decompress and combine .gz and paired end files as required logging . info ( 'Decompressing and combining .fastq files for CLARK analysis' ) fileprep . Fileprep ( self ) else : logging . info ( 'Using .fasta files for CLARK analysis' ) for sample in self . runmetadata . samples : sample . general . combined = sample . general . fastqfiles [ 0 ] | Create objects to store data and metadata for each sample . Also perform necessary file manipulations | 135 | 17 |
15,712 | def settargets ( self ) : # Define the set targets call. Include the path to the script, the database path and files, as well # as the taxonomic rank to use logging . info ( 'Setting up database' ) self . targetcall = 'cd {} && ./set_targets.sh {} {} --{}' . format ( self . clarkpath , self . databasepath , self . database , self . rank ) # subprocess . call ( self . targetcall , shell = True , stdout = self . devnull , stderr = self . devnull ) | Set the targets to be used in the analyses . Involves the path of the database files the database files to use and the level of classification for the analysis | 129 | 31 |
15,713 | def classifymetagenome ( self ) : logging . info ( 'Classifying metagenomes' ) # Define the system call self . classifycall = 'cd {} && ./classify_metagenome.sh -O {} -R {} -n {} --light' . format ( self . clarkpath , self . filelist , self . reportlist , self . cpus ) # Variable to store classification state classify = True for sample in self . runmetadata . samples : try : # Define the name of the .csv classification file sample . general . classification = sample . general . combined . split ( '.' ) [ 0 ] + '.csv' # If the file exists, then set classify to False if os . path . isfile ( sample . general . classification ) : classify = False except KeyError : pass # Run the system call if the samples have not been classified if classify : # Run the call subprocess . call ( self . classifycall , shell = True , stdout = self . devnull , stderr = self . devnull ) | Run the classify metagenome of the CLARK package on the samples | 221 | 14 |
15,714 | def lists ( self ) : # Prepare the lists to be used to classify the metagenomes with open ( self . filelist , 'w' ) as filelist : with open ( self . reportlist , 'w' ) as reportlist : for sample in self . runmetadata . samples : if self . extension == 'fastq' : try : status = sample . run . Description if status == 'metagenome' : filelist . write ( sample . general . combined + '\n' ) reportlist . write ( sample . general . combined . split ( '.' ) [ 0 ] + '\n' ) except AttributeError : pass else : if sample . general . combined != 'NA' : filelist . write ( sample . general . combined + '\n' ) reportlist . write ( sample . general . combined . split ( '.' ) [ 0 ] + '\n' ) | Prepare the list of files to be processed | 190 | 9 |
15,715 | def estimateabundance ( self ) : logging . info ( 'Estimating abundance of taxonomic groups' ) # Create and start threads for i in range ( self . cpus ) : # Send the threads to the appropriate destination function threads = Thread ( target = self . estimate , args = ( ) ) # Set the daemon to true - something to do with thread management threads . setDaemon ( True ) # Start the threading threads . start ( ) with progressbar ( self . runmetadata . samples ) as bar : for sample in bar : try : if sample . general . combined != 'NA' : # Set the name of the abundance report sample . general . abundance = sample . general . combined . split ( '.' ) [ 0 ] + '_abundance.csv' # if not hasattr(sample, 'commands'): if not sample . commands . datastore : sample . commands = GenObject ( ) # Define system calls sample . commands . target = self . targetcall sample . commands . classify = self . classifycall sample . commands . abundancecall = 'cd {} && ./estimate_abundance.sh -D {} -F {} > {}' . format ( self . clarkpath , self . databasepath , sample . general . classification , sample . general . abundance ) self . abundancequeue . put ( sample ) except KeyError : pass self . abundancequeue . join ( ) | Estimate the abundance of taxonomic groups | 299 | 8 |
15,716 | def get_command_templates ( command_tokens , file_tokens = [ ] , path_tokens = [ ] , job_options = [ ] ) : files = get_files ( file_tokens ) paths = get_paths ( path_tokens ) job_options = get_options ( job_options ) templates = _get_command_templates ( command_tokens , files , paths , job_options ) for command_template in templates : command_template . _dependencies = _get_prelim_dependencies ( command_template , templates ) return templates | Given a list of tokens from the grammar return a list of commands . | 134 | 14 |
15,717 | def get_files ( file_tokens , cwd = None ) : if not file_tokens : return [ ] token = file_tokens . pop ( ) try : filename = token . filename except AttributeError : filename = '' if cwd : input = Input ( token . alias , filename , cwd = cwd ) else : input = Input ( token . alias , filename ) return [ input ] + get_files ( file_tokens ) | Given a list of parser file tokens return a list of input objects for them . | 101 | 16 |
15,718 | def get_paths ( path_tokens ) : if len ( path_tokens ) == 0 : return [ ] token = path_tokens . pop ( ) path = PathToken ( token . alias , token . path ) return [ path ] + get_paths ( path_tokens ) | Given a list of parser path tokens return a list of path objects for them . | 68 | 16 |
15,719 | def _get_command_templates ( command_tokens , files = [ ] , paths = [ ] , job_options = [ ] , count = 1 ) : if not command_tokens : return [ ] comment_tokens , command_token = command_tokens . pop ( ) parts = [ ] parts += job_options + _get_comments ( comment_tokens ) for part in command_token [ 0 ] : # Check for file try : parts . append ( _get_file_by_alias ( part , files ) ) continue except ( AttributeError , ValueError ) : pass # Check for path/string for cut in part . split ( ) : try : parts . append ( _get_path_by_name ( cut , paths ) ) continue except ValueError : pass parts . append ( cut ) command_template = CommandTemplate ( alias = str ( count ) , parts = parts ) [ setattr ( p , 'alias' , command_template . alias ) for p in command_template . output_parts ] return [ command_template ] + _get_command_templates ( command_tokens , files , paths , job_options , count + 1 ) | Reversivly create command templates . | 259 | 8 |
15,720 | def _get_prelim_dependencies ( command_template , all_templates ) : deps = [ ] for input in command_template . input_parts : if '.' not in input . alias : continue for template in all_templates : for output in template . output_parts : if input . fuzzy_match ( output ) : deps . append ( template ) break return list ( set ( deps ) ) | Given a command_template determine which other templates it depends on . This should not be used as the be - all end - all of dependencies and before calling each command ensure that it s requirements are met . | 91 | 41 |
15,721 | def _is_output ( part ) : if part [ 0 ] . lower ( ) == 'o' : return True elif part [ 0 ] [ : 2 ] . lower ( ) == 'o:' : return True elif part [ 0 ] [ : 2 ] . lower ( ) == 'o.' : return True else : return False | Returns whether the given part represents an output variable . | 71 | 10 |
15,722 | def search_browser ( self , text ) : self . impl . get ( self . base_url ) search_div = self . impl . find_element_by_id ( "search" ) search_term = search_div . find_element_by_id ( "term" ) search_term . send_keys ( text ) search_div . find_element_by_id ( "submit" ) . click ( ) e = self . impl . find_element_by_css_selector ( "table.list tr td a" ) return e . get_attribute ( "href" ) | do a slow search via the website and return the first match | 129 | 12 |
15,723 | def search_fast ( self , text ) : resp = self . impl . get ( "{base_url}/{text}/json" . format ( base_url = self . base_url , text = text ) ) return resp . json ( ) [ "info" ] [ "package_url" ] | do a sloppy quick search via the json index | 66 | 9 |
15,724 | def main ( search , query ) : url = search . search ( query ) print ( url ) search . open_page ( url ) | main function that does the search | 28 | 6 |
15,725 | def cli_main ( ) : SearchContext . commit ( ) args = parser . parse_args ( ) # open up a browser firefox_remote = Remote ( "http://127.0.0.1:4444/wd/hub" , DesiredCapabilities . FIREFOX ) with contextlib . closing ( firefox_remote ) : context = SearchContext . from_instances ( [ FastSearch ( ) , Browser ( firefox_remote ) ] ) search = Search ( parent = context ) if args . fast : with context . use ( FastSearch , Browser ) : main ( search , args . query ) else : with context . use ( Browser ) : main ( search , args . query ) | cli entrypoitns sets up everything needed | 149 | 9 |
15,726 | def camel_to_underscore ( name ) : name = re . sub ( r'(?<!\b)(?<!_)([A-Z][a-z])' , r'_\1' , name ) name = re . sub ( r'(?<!\b)(?<!_)([a-z])([A-Z])' , r'\1_\2' , name ) name = name . lower ( ) return name | Convert camel case name to underscore name . | 104 | 9 |
15,727 | def main_func ( args = None ) : # we have to initialize a gui even if we dont need one right now. # as soon as you call maya.standalone.initialize(), a QApplication # with type Tty is created. This is the type for conosle apps. # Because i have not found a way to replace that, we just init the gui. guimain . init_gui ( ) main . init ( ) launcher = Launcher ( ) parsed , unknown = launcher . parse_args ( args ) parsed . func ( parsed , unknown ) | Main funcion when executing this module as script | 119 | 9 |
15,728 | def setup_launch_parser ( self , parser ) : parser . set_defaults ( func = self . launch ) parser . add_argument ( "addon" , help = "The jukebox addon to launch. The addon should be a standalone plugin." ) | Setup the given parser for the launch command | 55 | 8 |
15,729 | def parse_args ( self , args = None ) : if args is None : args = sys . argv [ 1 : ] return self . parser . parse_known_args ( args ) | Parse the given arguments | 40 | 5 |
15,730 | def list_objects ( self , prefix = None , delimiter = None ) : return self . _client . list_objects ( instance = self . _instance , bucket_name = self . name , prefix = prefix , delimiter = delimiter ) | List the objects for this bucket . | 52 | 7 |
15,731 | def upload_object ( self , object_name , file_obj ) : return self . _client . upload_object ( self . _instance , self . name , object_name , file_obj ) | Upload an object to this bucket . | 43 | 7 |
15,732 | def delete_object ( self , object_name ) : self . _client . remove_object ( self . _instance , self . name , object_name ) | Remove an object from this bucket . | 34 | 7 |
15,733 | def objects ( self ) : return [ ObjectInfo ( o , self . _instance , self . _bucket , self . _client ) for o in self . _proto . object ] | The objects in this listing . | 40 | 6 |
15,734 | def delete ( self ) : self . _client . remove_object ( self . _instance , self . _bucket , self . name ) | Remove this object . | 30 | 4 |
15,735 | def download ( self ) : return self . _client . download_object ( self . _instance , self . _bucket , self . name ) | Download this object . | 31 | 4 |
15,736 | def upload ( self , file_obj ) : return self . _client . upload_object ( self . _instance , self . _bucket , self . name , file_obj ) | Replace the content of this object . | 39 | 8 |
15,737 | def moving_average ( arr : np . ndarray , n : int = 3 ) -> np . ndarray : ret = np . cumsum ( arr , dtype = float ) ret [ n : ] = ret [ n : ] - ret [ : - n ] return ret [ n - 1 : ] / n | Calculate the moving overage over an array . | 69 | 11 |
15,738 | def recursive_getattr ( obj : Any , attr : str , * args ) -> Any : def _getattr ( obj , attr ) : return getattr ( obj , attr , * args ) return functools . reduce ( _getattr , [ obj ] + attr . split ( '.' ) ) | Recursive getattar . | 68 | 6 |
15,739 | def recursive_setattr ( obj : Any , attr : str , val : Any ) -> Any : pre , _ , post = attr . rpartition ( '.' ) return setattr ( recursive_getattr ( obj , pre ) if pre else obj , post , val ) | Recusrive setattr . | 60 | 6 |
15,740 | def recursive_getitem ( d : Mapping [ str , Any ] , keys : Union [ str , Sequence [ str ] ] ) -> Any : # If only a string, then just just return the item if isinstance ( keys , str ) : return d [ keys ] else : return functools . reduce ( operator . getitem , keys , d ) | Recursively retrieve an item from a nested dict . | 75 | 11 |
15,741 | def get_array_for_fit ( observables : dict , track_pt_bin : int , jet_pt_bin : int ) -> histogram . Histogram1D : for name , observable in observables . items ( ) : if observable . track_pt_bin == track_pt_bin and observable . jet_pt_bin == jet_pt_bin : return histogram . Histogram1D . from_existing_hist ( observable . hist ) raise ValueError ( "Cannot find fit with jet pt bin {jet_pt_bin} and track pt bin {track_pt_bin}" ) | Get a Histogram1D associated with the selected jet and track pt bins . | 131 | 16 |
15,742 | def epcrparsethreads ( self ) : from Bio import SeqIO # Create the threads for the BLAST analysis for sample in self . metadata : if sample . general . bestassemblyfile != 'NA' : threads = Thread ( target = self . epcrparse , args = ( ) ) threads . setDaemon ( True ) threads . start ( ) for sample in self . metadata : if sample . general . bestassemblyfile != 'NA' : if sample [ self . analysistype ] . primers != 'NA' : # Initialise a dictionary to store the SeqIO records of each assembly record = dict ( ) # Initialise dictionaries to store results in the object sample [ self . analysistype ] . blastresults = dict ( ) sample [ self . analysistype ] . rawblastresults = dict ( ) # Load the records from the assembly into the dictionary for rec in SeqIO . parse ( sample . general . bestassemblyfile , 'fasta' ) : record [ rec . id ] = str ( rec . seq ) # Iterate through the ePCR results for line in sample [ self . analysistype ] . epcrresults : # The data of interest is in the lines that do not start with a # # TLH 2016-SEQ-0359_4_length_321195_cov_28.6354_ID_3773 + 227879 228086 0 0 208/1000-1000 if not line . startswith ( '#' ) : # Add the variables to the queue self . epcrparsequeue . put ( ( sample , record , line ) ) self . epcrparsequeue . join ( ) | Parse the ePCR results and run BLAST on the parsed results | 357 | 15 |
15,743 | def epcrparse ( self ) : from Bio . Blast . Applications import NcbiblastnCommandline while True : sample , record , line = self . epcrparsequeue . get ( ) # Split the data on tabs gene , chromosome , strand , start , end , m_match , gaps , act_len_exp_len = line . split ( '\t' ) # Extract the gene sequence from the contigs # The record dictionary has the contig name, and the sequence. Splice out the data using the start and # end coordinates specified by ePCR genesequence = record [ chromosome ] [ int ( start ) - 1 : int ( end ) ] # Set up BLASTn using blastn-short, as the probe sequences tend to be very short blastn = NcbiblastnCommandline ( db = sample [ self . analysistype ] . probes . split ( '.' ) [ 0 ] , num_threads = 12 , task = 'blastn-short' , num_alignments = 1 , outfmt = "'6 qseqid sseqid positive mismatch gaps " "evalue bitscore slen length'" ) # Run the BLASTn, with the gene sequence as stdin out , err = blastn ( stdin = genesequence ) # Split the output string on tabs results = out . rstrip ( ) . split ( '\t' ) # Populate the raw blast results sample [ self . analysistype ] . rawblastresults [ gene ] = results # Create named variables from the list positives = float ( results [ 2 ] ) mismatches = float ( results [ 3 ] ) gaps = float ( results [ 4 ] ) subjectlength = float ( results [ 7 ] ) # Calculate the percent identity percentidentity = float ( '{:0.2f}' . format ( ( positives - gaps ) / subjectlength * 100 ) ) # Create a dictionary with the desired values to store in the metadata object resultdict = { 'matches' : positives , 'mismatches' : mismatches , 'gaps' : gaps , 'subject_length' : subjectlength , 'percent_identity' : percentidentity , 'match_length' : results [ 8 ] . split ( '\n' ) [ 0 ] } # Populate the metadata object with the dictionary sample [ self . analysistype ] . blastresults [ gene ] = resultdict self . epcrparsequeue . task_done ( ) | Run BLAST and record results to the object | 527 | 9 |
15,744 | def report ( self ) : # Initialise a variable to store the results data = '' for sample in self . metadata : if sample [ self . analysistype ] . primers != 'NA' : # Set the name of the strain-specific report sample [ self . analysistype ] . report = os . path . join ( sample [ self . analysistype ] . reportdir , '{}_{}.csv' . format ( sample . name , self . analysistype ) ) # Populate the strain-specific string with header, and strain name strainspecific = 'Strain,{},\n{},' . format ( ',' . join ( sorted ( sample [ self . analysistype ] . targets ) ) , sample . name ) # Iterate through all the genes in the organism-specific analysis for gene in sorted ( sample [ self . analysistype ] . targets ) : try : # Extract the percent identity percentidentity = sample [ self . analysistype ] . blastresults [ gene ] [ 'percent_identity' ] # If the % identity is greater than the cutoff of 50%, the gene is considered to be present if percentidentity > 50 : strainspecific += '{},' . format ( percentidentity ) else : strainspecific += '-,' # If there are no BLAST results, then the gene is absent except KeyError : strainspecific += '-,' strainspecific += '\n' # Open and write the data to the strain-specific report with open ( sample [ self . analysistype ] . report , 'w' ) as specificreport : specificreport . write ( strainspecific ) # Add all the data from each strain to the cumulative data string data += strainspecific # Open and write the cumulative data to the cumulative report with open ( os . path . join ( self . reportdir , '{}.csv' . format ( self . analysistype ) ) , 'w' ) as report : report . write ( data ) | Create reports of the findings | 420 | 5 |
15,745 | def setup_environment ( ) : osinter = ostool . get_interface ( ) pypath = osinter . get_maya_envpath ( ) for p in sys . path : pypath = os . pathsep . join ( ( pypath , p ) ) os . environ [ 'PYTHONPATH' ] = pypath | Set up neccessary environment variables | 78 | 7 |
15,746 | def execute_mayapy ( args , wait = True ) : osinter = ostool . get_interface ( ) mayapy = osinter . get_maya_python ( ) allargs = [ mayapy ] allargs . extend ( args ) print "Executing mayapy with: %s" % allargs mayapyprocess = subprocess . Popen ( allargs ) if wait : rc = mayapyprocess . wait ( ) print "Process mayapy finished!" return rc else : return mayapyprocess | Execute mayapython with the given arguments capture and return the output | 106 | 14 |
15,747 | def setDoc ( self , doc ) : self . ui . overAtten . setNum ( doc [ 'overloaded_attenuation' ] ) # also set composite stim type # self.ui.traceType.setText(doc['testtype']) self . ui . componentDetails . clearDoc ( ) self . ui . componentDetails . setDoc ( doc [ 'components' ] ) | Presents the documentation | 86 | 4 |
15,748 | def increase_by_changes ( self , changes_amount , ratio ) : increases = round ( changes_amount * ratio ) return self . increase ( int ( increases ) ) | Increase version by amount of changes | 36 | 6 |
15,749 | def wrap_maya_ui ( mayaname ) : ptr = apiUI . MQtUtil . findControl ( mayaname ) if ptr is None : ptr = apiUI . MQtUtil . findLayout ( mayaname ) if ptr is None : ptr = apiUI . MQtUtil . findMenuItem ( mayaname ) if ptr is not None : return wrap ( long ( ptr ) ) | Given the name of a Maya UI element of any type return the corresponding QWidget or QAction . If the object does not exist returns None | 92 | 28 |
15,750 | def query_args ( self , name ) : sql = 'select type, id from code_items ' 'where kind = 22 and name = ?' logging . debug ( '%s %s' , sql , ( name , ) ) self . cursor . execute ( sql , ( name , ) ) func = self . cursor . fetchone ( ) if func : sql = 'select param_number, type, name ' 'from code_items where parent_id = ?' logging . debug ( '%s %s' , sql , ( func [ 1 ] , ) ) self . cursor . execute ( sql , ( func [ 1 ] , ) ) args = self . cursor . fetchall ( ) ret_type = clean_ret_type ( func [ 0 ] ) args = [ ( arg_number , sanitize_type ( arg_type ) , arg_name ) for arg_number , arg_type , arg_name in args ] return ret_type , name , args return None | Query the return type and argument list of the specified function in the specified database . | 210 | 16 |
15,751 | def query_info ( self , name , like , kind ) : kind = self . _make_kind_id ( kind ) # Database from VS2015 does not have assoc_text. # # sql = 'select name, kind, file_id, type, assoc_text ' \ # 'from code_items ' \ # 'where name {} ?'.format('like' if like else '=') sql = 'select name, kind, file_id, type ' 'from code_items ' 'where name {} ?' . format ( 'like' if like else '=' ) args = ( name , ) if like : sql += ' escape ?' args = ( name , '\\' ) if kind : sql += ' and kind = ?' args = ( name , kind ) if like and kind : args = ( name , '\\' , kind ) logging . debug ( '%s %s' , sql , args ) self . cursor . execute ( sql , args ) return self . cursor . fetchall ( ) , self | Query the information of the name in the database . | 219 | 10 |
15,752 | def query_names ( self , name , like , kind ) : kind = self . _make_kind_id ( kind ) sql = 'select id, name from files ' 'where leaf_name {} ?' . format ( 'like' if like else '=' ) args = ( name , ) if like : sql += ' escape ?' args = ( name , '\\' ) logging . debug ( '%s %s' , sql , args ) self . cursor . execute ( sql , args ) ids = self . cursor . fetchall ( ) files = [ ] for file_id , header in ids : sql = 'select name from code_items ' 'where file_id = ?' args = ( file_id , ) if kind : sql += 'and kind = ?' args = ( file_id , kind ) logging . debug ( '%s %s' , sql , args ) self . cursor . execute ( sql , args ) files . append ( ( header , self . cursor . fetchall ( ) ) ) return files | Query function declarations in the files . | 221 | 7 |
15,753 | def query_struct ( self , name ) : sql = 'select id, file_id, name from code_items ' 'where name = ?' self . cursor . execute ( sql , ( name , ) ) for i in self . cursor . fetchall ( ) : sql = 'select id, type, name from code_items ' 'where parent_id = ?' self . cursor . execute ( sql , ( i [ 0 ] , ) ) members = self . cursor . fetchall ( ) if members : print ( self . file_id_to_name ( i [ 1 ] ) , i [ 2 ] ) print ( members ) | Query struct . | 135 | 3 |
15,754 | def file_id_to_name ( self , file_id ) : sql = 'select name from files where id = ?' logging . debug ( '%s %s' , sql , ( file_id , ) ) self . cursor . execute ( sql , ( file_id , ) ) name = self . cursor . fetchone ( ) if name : return name [ 0 ] return '' | Convert a file id to the file name . | 83 | 10 |
15,755 | def _make_kind_id ( self , name_or_id ) : if not name_or_id : return None if name_or_id . isdigit ( ) : return name_or_id return self . kind_name_to_id ( name_or_id ) | Make kind_id from kind_name or kind_id . | 62 | 13 |
15,756 | def query_kinds ( self , kind ) : logging . debug ( _ ( 'querying %s' ) , kind ) if kind is None : return self . _kind_id_to_name . items ( ) if kind . isdigit ( ) : kind_name = self . kind_id_to_name ( int ( kind ) ) if kind_name : kind = ( kind , kind_name ) else : logging . warning ( _ ( 'id not found: %s' ) , kind ) kind = None else : kind_id = self . kind_name_to_id ( kind ) if kind_id : kind = ( kind_id , kind ) else : logging . warning ( _ ( 'name not found: %s' ) , kind ) kind = None return [ kind ] | Query kinds . | 170 | 3 |
15,757 | def _init_kind_converter ( self ) : from . . utils import invert_dict kinds = self . session . query ( Kind ) . all ( ) self . _kind_id_to_name = { kind . id : kind . name for kind in kinds } self . _kind_name_to_id = invert_dict ( self . _kind_id_to_name ) | Make a dictionary mapping kind ids to the names . | 88 | 11 |
15,758 | def make_export ( self , exports ) : sql = 'drop table if exists export' logging . debug ( sql ) self . cursor . execute ( sql ) sql = 'create table if not exists export ' '(func text unique, module text)' logging . debug ( sql ) self . cursor . execute ( sql ) for module in exports : logging . debug ( _ ( 'insering exports from %s' ) , module ) sql = 'insert into export values (?, ?)' for func in exports [ module ] : if func : try : self . cursor . execute ( sql , ( func , module ) ) except sqlite3 . IntegrityError : pass self . con . commit ( ) | Populate library exported function data . | 141 | 7 |
15,759 | def query_func_module ( self , func ) : exp = self . session . query ( Export ) . filter_by ( func = func ) . first ( ) if exp : return exp logging . debug ( _ ( 'Function not found: %s' ) , func ) alt = func + 'A' exp = self . session . query ( Export ) . filter_by ( func = alt ) . first ( ) if exp : logging . warning ( _ ( 'Using ANSI version: %s' ) , alt ) return exp logging . warning ( _ ( 'Not handled: %s or %s' ) , func , alt ) return None | Query the module name of the specified function . | 136 | 9 |
15,760 | def query_module_funcs ( self , module ) : funcs = self . session . query ( Export ) . filter_by ( module = module ) . all ( ) return funcs | Query the functions in the specified module . | 40 | 8 |
15,761 | def _build_named_object_ids ( parameters ) : if isinstance ( parameters , str ) : return [ _build_named_object_id ( parameters ) ] return [ _build_named_object_id ( parameter ) for parameter in parameters ] | Builds a list of NamedObjectId . | 54 | 9 |
15,762 | def _build_command_ids ( issued_commands ) : if isinstance ( issued_commands , IssuedCommand ) : entry = issued_commands . _proto . commandQueueEntry return [ entry . cmdId ] else : return [ issued_command . _proto . commandQueueEntry . cmdId for issued_command in issued_commands ] | Builds a list of CommandId . | 77 | 8 |
15,763 | def _cache_key ( cmd_id ) : return '{}__{}__{}__{}' . format ( cmd_id . generationTime , cmd_id . origin , cmd_id . sequenceNumber , cmd_id . commandName ) | commandId is a tuple . Make a unique key for it . | 55 | 13 |
15,764 | def get_command_history ( self , issued_command ) : #pylint: disable=protected-access entry = issued_command . _proto . commandQueueEntry key = self . _cache_key ( entry . cmdId ) if key in self . _cache : return self . _cache [ key ] return None | Gets locally cached CommandHistory for the specified command . | 69 | 11 |
15,765 | def add ( self , parameters , abort_on_invalid = True , send_from_cache = True ) : # Verify that we already know our assigned subscription_id assert self . subscription_id != - 1 if not parameters : return options = web_pb2 . ParameterSubscriptionRequest ( ) options . subscriptionId = self . subscription_id options . abortOnInvalid = abort_on_invalid options . sendFromCache = send_from_cache options . id . extend ( _build_named_object_ids ( parameters ) ) self . _manager . send ( 'subscribe' , options ) | Add one or more parameters to this subscription . | 129 | 9 |
15,766 | def remove ( self , parameters ) : # Verify that we already know our assigned subscription_id assert self . subscription_id != - 1 if not parameters : return options = web_pb2 . ParameterSubscriptionRequest ( ) options . subscriptionId = self . subscription_id options . id . extend ( _build_named_object_ids ( parameters ) ) self . _manager . send ( 'unsubscribe' , options ) | Remove one or more parameters from this subscription . | 90 | 9 |
15,767 | def set_parameter_value ( self , parameter , value ) : parameter = adapt_name_for_rest ( parameter ) url = '/processors/{}/{}/parameters{}' . format ( self . _instance , self . _processor , parameter ) req = _build_value_proto ( value ) self . _client . put_proto ( url , data = req . SerializeToString ( ) ) | Sets the value of the specified parameter . | 94 | 9 |
15,768 | def set_parameter_values ( self , values ) : req = rest_pb2 . BulkSetParameterValueRequest ( ) for key in values : item = req . request . add ( ) item . id . MergeFrom ( _build_named_object_id ( key ) ) item . value . MergeFrom ( _build_value_proto ( values [ key ] ) ) url = '/processors/{}/{}/parameters/mset' . format ( self . _instance , self . _processor ) self . _client . post_proto ( url , data = req . SerializeToString ( ) ) | Sets the value of multiple parameters . | 135 | 8 |
15,769 | def issue_command ( self , command , args = None , dry_run = False , comment = None ) : req = rest_pb2 . IssueCommandRequest ( ) req . sequenceNumber = SequenceGenerator . next ( ) req . origin = socket . gethostname ( ) req . dryRun = dry_run if comment : req . comment = comment if args : for key in args : assignment = req . assignment . add ( ) assignment . name = key assignment . value = str ( args [ key ] ) command = adapt_name_for_rest ( command ) url = '/processors/{}/{}/commands{}' . format ( self . _instance , self . _processor , command ) response = self . _client . post_proto ( url , data = req . SerializeToString ( ) ) proto = rest_pb2 . IssueCommandResponse ( ) proto . ParseFromString ( response . content ) return IssuedCommand ( proto , self ) | Issue the given command | 209 | 4 |
15,770 | def list_alarms ( self , start = None , stop = None ) : # TODO implement continuation token on server params = { 'order' : 'asc' } if start is not None : params [ 'start' ] = to_isostring ( start ) if stop is not None : params [ 'stop' ] = to_isostring ( stop ) # Server does not do pagination on listings of this resource. # Return an iterator anyway for similarity with other API methods url = '/processors/{}/{}/alarms' . format ( self . _instance , self . _processor ) response = self . _client . get_proto ( path = url , params = params ) message = rest_pb2 . ListAlarmsResponse ( ) message . ParseFromString ( response . content ) alarms = getattr ( message , 'alarm' ) return iter ( [ Alarm ( alarm ) for alarm in alarms ] ) | Lists the active alarms . | 201 | 6 |
15,771 | def set_default_calibrator ( self , parameter , type , data ) : # pylint: disable=W0622 req = mdb_pb2 . ChangeParameterRequest ( ) req . action = mdb_pb2 . ChangeParameterRequest . SET_DEFAULT_CALIBRATOR if type : _add_calib ( req . defaultCalibrator , type , data ) url = '/mdb/{}/{}/parameters/{}' . format ( self . _instance , self . _processor , parameter ) response = self . _client . post_proto ( url , data = req . SerializeToString ( ) ) | Apply a calibrator while processing raw values of the specified parameter . If there is already a default calibrator associated to this parameter that calibrator gets replaced . | 143 | 31 |
15,772 | def reset_calibrators ( self , parameter ) : req = mdb_pb2 . ChangeParameterRequest ( ) req . action = mdb_pb2 . ChangeParameterRequest . RESET_CALIBRATORS calib_info = req . defaultCalibrator url = '/mdb/{}/{}/parameters/{}' . format ( self . _instance , self . _processor , parameter ) response = self . _client . post_proto ( url , data = req . SerializeToString ( ) ) | Reset all calibrators for the specified parameter to their original MDB value . | 116 | 16 |
15,773 | def set_default_alarm_ranges ( self , parameter , watch = None , warning = None , distress = None , critical = None , severe = None , min_violations = 1 ) : req = mdb_pb2 . ChangeParameterRequest ( ) req . action = mdb_pb2 . ChangeParameterRequest . SET_DEFAULT_ALARMS if ( watch or warning or distress or critical or severe ) : _add_alarms ( req . defaultAlarm , watch , warning , distress , critical , severe , min_violations ) url = '/mdb/{}/{}/parameters/{}' . format ( self . _instance , self . _processor , parameter ) response = self . _client . post_proto ( url , data = req . SerializeToString ( ) ) | Generate out - of - limit alarms for a parameter using the specified alarm ranges . | 176 | 17 |
15,774 | def reset_alarm_ranges ( self , parameter ) : req = mdb_pb2 . ChangeParameterRequest ( ) req . action = mdb_pb2 . ChangeParameterRequest . RESET_ALARMS url = '/mdb/{}/{}/parameters/{}' . format ( self . _instance , self . _processor , parameter ) response = self . _client . post_proto ( url , data = req . SerializeToString ( ) ) | Reset all alarm limits for the specified parameter to their original MDB value . | 105 | 16 |
15,775 | def acknowledge_alarm ( self , alarm , comment = None ) : url = '/processors/{}/{}/parameters{}/alarms/{}' . format ( self . _instance , self . _processor , alarm . name , alarm . sequence_number ) req = rest_pb2 . EditAlarmRequest ( ) req . state = 'acknowledged' if comment is not None : req . comment = comment self . _client . put_proto ( url , data = req . SerializeToString ( ) ) | Acknowledges a specific alarm associated with a parameter . | 117 | 10 |
15,776 | def create_command_history_subscription ( self , issued_command = None , on_data = None , timeout = 60 ) : options = web_pb2 . CommandHistorySubscriptionRequest ( ) options . ignorePastCommands = True if issued_command : options . commandId . extend ( _build_command_ids ( issued_command ) ) manager = WebSocketSubscriptionManager ( self . _client , resource = 'cmdhistory' , options = options ) # Represent subscription as a future subscription = CommandHistorySubscription ( manager ) wrapped_callback = functools . partial ( _wrap_callback_parse_cmdhist_data , subscription , on_data ) manager . open ( wrapped_callback , instance = self . _instance , processor = self . _processor ) # Wait until a reply or exception is received subscription . reply ( timeout = timeout ) return subscription | Create a new command history subscription . | 183 | 7 |
15,777 | def create_parameter_subscription ( self , parameters , on_data = None , abort_on_invalid = True , update_on_expiration = False , send_from_cache = True , timeout = 60 ) : options = web_pb2 . ParameterSubscriptionRequest ( ) options . subscriptionId = - 1 # This means 'create a new subscription' options . abortOnInvalid = abort_on_invalid options . updateOnExpiration = update_on_expiration options . sendFromCache = send_from_cache options . id . extend ( _build_named_object_ids ( parameters ) ) manager = WebSocketSubscriptionManager ( self . _client , resource = 'parameter' , options = options ) # Represent subscription as a future subscription = ParameterSubscription ( manager ) wrapped_callback = functools . partial ( _wrap_callback_parse_parameter_data , subscription , on_data ) manager . open ( wrapped_callback , instance = self . _instance , processor = self . _processor ) # Wait until a reply or exception is received subscription . reply ( timeout = timeout ) return subscription | Create a new parameter subscription . | 242 | 6 |
15,778 | def create_alarm_subscription ( self , on_data = None , timeout = 60 ) : manager = WebSocketSubscriptionManager ( self . _client , resource = 'alarms' ) # Represent subscription as a future subscription = AlarmSubscription ( manager ) wrapped_callback = functools . partial ( _wrap_callback_parse_alarm_data , subscription , on_data ) manager . open ( wrapped_callback , instance = self . _instance , processor = self . _processor ) # Wait until a reply or exception is received subscription . reply ( timeout = timeout ) return subscription | Create a new alarm subscription . | 126 | 6 |
15,779 | def get_by ( self , name ) : return next ( ( item for item in self if item . name == name ) , None ) | get element by name | 29 | 4 |
15,780 | def fastqc ( self ) : while True : # while daemon threadlock = threading . Lock ( ) # Unpack the variables from the queue ( sample , systemcall , outputdir , fastqcreads ) = self . qcqueue . get ( ) # Check to see if the output HTML file already exists try : _ = glob ( os . path . join ( outputdir , '*.html' ) ) [ 0 ] except IndexError : # Make the output directory make_path ( outputdir ) # Run the system calls outstr = str ( ) errstr = str ( ) out , err = run_subprocess ( systemcall ) outstr += out errstr += err out , err = run_subprocess ( fastqcreads ) outstr += out errstr += err # Acquire thread lock, and write the logs to file threadlock . acquire ( ) write_to_logfile ( systemcall , systemcall , self . logfile , sample . general . logout , sample . general . logerr , None , None ) write_to_logfile ( fastqcreads , fastqcreads , self . logfile , sample . general . logout , sample . general . logerr , None , None ) write_to_logfile ( outstr , errstr , self . logfile , sample . general . logout , sample . general . logerr , None , None ) threadlock . release ( ) # Rename the outputs try : shutil . move ( os . path . join ( outputdir , 'stdin_fastqc.html' ) , os . path . join ( outputdir , '{}_fastqc.html' . format ( sample . name ) ) ) shutil . move ( os . path . join ( outputdir , 'stdin_fastqc.zip' ) , os . path . join ( outputdir , '{}_fastqc.zip' . format ( sample . name ) ) ) except IOError : pass # Signal to qcqueue that job is done self . qcqueue . task_done ( ) | Run fastqc system calls | 442 | 6 |
15,781 | def trimquality ( self ) : logging . info ( "Trimming fastq files" ) # Iterate through strains with fastq files with progressbar ( self . metadata ) as bar : for sample in bar : # As the metadata can be populated with 'NA' (string) if there are no fastq files, only process if # :fastqfiles is a list if type ( sample . general . fastqfiles ) is list : # Check to see if the fastq files exist fastqfiles = sorted ( sample . general . fastqfiles ) # Define the output directory outputdir = sample . general . outputdirectory # Define the name of the trimmed fastq files cleanforward = os . path . join ( outputdir , '{}_R1_trimmed.fastq.gz' . format ( sample . name ) ) cleanreverse = os . path . join ( outputdir , '{}_R2_trimmed.fastq.gz' . format ( sample . name ) ) # Incorporate read length into the minlength parameter - set it to 50 unless one or more of the # reads has a lower calculated length than 50 try : lesser_length = min ( int ( sample . run . forwardlength ) , int ( sample . run . reverselength ) ) except ValueError : lesser_length = int ( sample . run . forwardlength ) min_len = 50 if lesser_length >= 50 else lesser_length # Initialise a variable to store the number of bases to automatically trim from the beginning of # each read, as these bases tend to have lower quality scores. If trimming the reads will cause trim_left = 0 # If, for some reason, only the reverse reads are present, use the appropriate output file name try : if 'R2' in fastqfiles [ 0 ] : if not os . path . isfile ( cleanreverse ) : out , err , bbdukcall = bbtools . bbduk_trim ( forward_in = fastqfiles [ 0 ] , reverse_in = None , forward_out = cleanreverse , trimq = 10 , minlength = min_len , forcetrimleft = trim_left , returncmd = True ) else : bbdukcall = str ( ) out = str ( ) err = str ( ) else : if not os . path . isfile ( cleanforward ) : out , err , bbdukcall = bbtools . bbduk_trim ( forward_in = fastqfiles [ 0 ] , forward_out = cleanforward , trimq = 10 , minlength = min_len , forcetrimleft = trim_left , returncmd = True ) else : bbdukcall = str ( ) out = str ( ) err = str ( ) except ( IndexError , CalledProcessError ) : bbdukcall = str ( ) out = str ( ) err = str ( ) # Write the command, stdout, and stderr to the logfile write_to_logfile ( bbdukcall , bbdukcall , self . logfile , sample . general . logout , sample . general . logerr , None , None ) write_to_logfile ( out , err , self . logfile , sample . general . logout , sample . general . logerr , None , None ) # Add the trimmed fastq files to a list trimmedfastqfiles = sorted ( glob ( os . path . join ( sample . general . outputdirectory , '*trimmed.fastq.gz' ) ) ) # Populate the metadata if the files exist sample . general . trimmedfastqfiles = trimmedfastqfiles if trimmedfastqfiles else list ( ) # Add all the trimmed files to the metadata logging . info ( 'Fastq files trimmed' ) | Uses bbduk from the bbmap tool suite to quality and adapter trim | 810 | 18 |
15,782 | def estimate_genome_size ( self ) : logging . info ( 'Estimating genome size using kmercountexact' ) for sample in self . metadata : # Initialise the name of the output file sample [ self . analysistype ] . peaksfile = os . path . join ( sample [ self . analysistype ] . outputdir , 'peaks.txt' ) # Run the kmer counting command out , err , cmd = bbtools . kmercountexact ( forward_in = sorted ( sample . general . fastqfiles ) [ 0 ] , peaks = sample [ self . analysistype ] . peaksfile , returncmd = True , threads = self . cpus ) # Set the command in the object sample [ self . analysistype ] . kmercountexactcmd = cmd # Extract the genome size from the peaks file sample [ self . analysistype ] . genomesize = bbtools . genome_size ( sample [ self . analysistype ] . peaksfile ) write_to_logfile ( out , err , self . logfile , sample . general . logout , sample . general . logerr , None , None ) | Use kmercountexact from the bbmap suite of tools to estimate the size of the genome | 247 | 21 |
15,783 | def error_correction ( self ) : logging . info ( 'Error correcting reads' ) for sample in self . metadata : sample . general . trimmedcorrectedfastqfiles = [ fastq . split ( '.fastq.gz' ) [ 0 ] + '_trimmed_corrected.fastq.gz' for fastq in sorted ( sample . general . fastqfiles ) ] try : if not os . path . isfile ( sample . general . trimmedcorrectedfastqfiles [ 0 ] ) : try : out , err , cmd = bbtools . tadpole ( forward_in = sorted ( sample . general . trimmedfastqfiles ) [ 0 ] , forward_out = sample . general . trimmedcorrectedfastqfiles [ 0 ] , returncmd = True , mode = 'correct' , threads = self . cpus ) # Set the command in the object sample [ self . analysistype ] . errorcorrectcmd = cmd write_to_logfile ( out = out , err = err , logfile = self . logfile , samplelog = sample . general . logout , sampleerr = sample . general . logerr , analysislog = None , analysiserr = None ) except IndexError : sample . general . trimmedcorrectedfastqfiles = list ( ) except CalledProcessError : sample . general . trimmedcorrectedfastqfiles = sample . general . trimmedfastqfiles except AttributeError : sample . general . trimmedcorrectedfastqfiles = list ( ) except IndexError : sample . general . trimmedcorrectedfastqfiles = list ( ) | Use tadpole from the bbmap suite of tools to perform error correction of the reads | 333 | 18 |
15,784 | def normalise_reads ( self ) : logging . info ( 'Normalising reads to a kmer depth of 100' ) for sample in self . metadata : # Set the name of the normalised read files sample . general . normalisedreads = [ fastq . split ( '.fastq.gz' ) [ 0 ] + '_normalised.fastq.gz' for fastq in sorted ( sample . general . fastqfiles ) ] try : # Run the normalisation command out , err , cmd = bbtools . bbnorm ( forward_in = sorted ( sample . general . trimmedcorrectedfastqfiles ) [ 0 ] , forward_out = sample . general . normalisedreads [ 0 ] , returncmd = True , threads = self . cpus ) sample [ self . analysistype ] . normalisecmd = cmd write_to_logfile ( out , err , self . logfile , sample . general . logout , sample . general . logerr , None , None ) except CalledProcessError : sample . general . normalisedreads = sample . general . trimmedfastqfiles except IndexError : sample . general . normalisedreads = list ( ) | Use bbnorm from the bbmap suite of tools to perform read normalisation | 247 | 17 |
15,785 | def merge_pairs ( self ) : logging . info ( 'Merging paired reads' ) for sample in self . metadata : # Can only merge paired-end if len ( sample . general . fastqfiles ) == 2 : # Set the name of the merged, and unmerged files sample . general . mergedreads = os . path . join ( sample . general . outputdirectory , '{}_paired.fastq.gz' . format ( sample . name ) ) sample . general . unmergedforward = os . path . join ( sample . general . outputdirectory , '{}_unpaired_R1.fastq.gz' . format ( sample . name ) ) sample . general . unmergedreverse = os . path . join ( sample . general . outputdirectory , '{}_unpaired_R2.fastq.gz' . format ( sample . name ) ) try : # Run the merging command - forward_in=sample.general.normalisedreads[0], out , err , cmd = bbtools . bbmerge ( forward_in = sorted ( sample . general . trimmedcorrectedfastqfiles ) [ 0 ] , merged_reads = sample . general . mergedreads , returncmd = True , outu1 = sample . general . unmergedforward , outu2 = sample . general . unmergedreverse , threads = self . cpus ) sample [ self . analysistype ] . bbmergecmd = cmd write_to_logfile ( out , err , self . logfile , sample . general . logout , sample . general . logerr , None , None ) except CalledProcessError : delattr ( sample . general , 'mergedreads' ) delattr ( sample . general , 'unmergedforward' ) delattr ( sample . general , 'unmergedreverse' ) except IndexError : delattr ( sample . general , 'mergedreads' ) delattr ( sample . general , 'unmergedforward' ) delattr ( sample . general , 'unmergedreverse' ) else : sample . general . mergedreads = sorted ( sample . general . trimmedcorrectedfastqfiles ) [ 0 ] | Use bbmerge from the bbmap suite of tools to merge paired - end reads | 466 | 19 |
15,786 | def main ( self ) : self . fasta_records ( ) self . fasta_stats ( ) self . find_largest_contig ( ) self . find_genome_length ( ) self . find_num_contigs ( ) self . find_n50 ( ) self . perform_pilon ( ) self . clear_attributes ( ) | Run all the methods required for pipeline outputs | 77 | 8 |
15,787 | def fasta_records ( self ) : for sample in self . metadata : # Create the analysis-type specific attribute setattr ( sample , self . analysistype , GenObject ( ) ) # Create a dictionary of records for each file try : record_dict = SeqIO . to_dict ( SeqIO . parse ( sample . general . bestassemblyfile , "fasta" ) ) except FileNotFoundError : record_dict = dict ( ) # Set the records dictionary as the attribute for the object sample [ self . analysistype ] . record_dict = record_dict | Use SeqIO to create dictionaries of all records for each FASTA file | 124 | 17 |
15,788 | def fasta_stats ( self ) : for sample in self . metadata : # Initialise variables to store appropriate values parsed from contig records contig_lengths = list ( ) fasta_sequence = str ( ) for contig , record in sample [ self . analysistype ] . record_dict . items ( ) : # Append the length of the contig to the list contig_lengths . append ( len ( record . seq ) ) # Add the contig sequence to the string fasta_sequence += record . seq # Set the reverse sorted (e.g. largest to smallest) list of contig sizes as the value sample [ self . analysistype ] . contig_lengths = sorted ( contig_lengths , reverse = True ) try : # Calculate the GC% of the total genome sequence using GC - format to have two decimal places sample [ self . analysistype ] . gc = float ( '{:0.2f}' . format ( GC ( fasta_sequence ) ) ) except TypeError : sample [ self . analysistype ] . gc = 'NA' | Parse the lengths of all contigs for each sample as well as the total GC% | 238 | 18 |
15,789 | def find_largest_contig ( self ) : # for file_name, contig_lengths in contig_lengths_dict.items(): for sample in self . metadata : # As the list is sorted in descending order, the largest contig is the first entry in the list sample [ self . analysistype ] . longest_contig = sample [ self . analysistype ] . contig_lengths | Determine the largest contig for each strain | 89 | 10 |
15,790 | def find_genome_length ( self ) : for sample in self . metadata : # Use the sum() method to add all the contig lengths in the list sample [ self . analysistype ] . genome_length = sum ( sample [ self . analysistype ] . contig_lengths ) | Determine the total length of all the contigs for each strain | 64 | 14 |
15,791 | def find_num_contigs ( self ) : for sample in self . metadata : # Use the len() method to count the number of entries in the list sample [ self . analysistype ] . num_contigs = len ( sample [ self . analysistype ] . contig_lengths ) | Count the total number of contigs for each strain | 64 | 10 |
15,792 | def find_n50 ( self ) : for sample in self . metadata : # Initialise the N50 attribute in case there is no assembly, and the attribute is not created in the loop sample [ self . analysistype ] . n50 = '-' # Initialise a variable to store a running total of contig lengths currentlength = 0 for contig_length in sample [ self . analysistype ] . contig_lengths : # Increment the current length with the length of the current contig currentlength += contig_length # If the current length is now greater than the total genome / 2, the current contig length is the N50 if currentlength >= sample [ self . analysistype ] . genome_length * 0.5 : # Populate the dictionary, and break the loop sample [ self . analysistype ] . n50 = contig_length break | Calculate the N50 for each strain . N50 is defined as the largest contig such that at least half of the total genome size is contained in contigs equal to or larger than this contig | 185 | 42 |
15,793 | def perform_pilon ( self ) : for sample in self . metadata : try : if sample [ self . analysistype ] . num_contigs > 500 or sample . confindr . contam_status == 'Contaminated' : sample . general . polish = False else : sample . general . polish = True except AttributeError : sample . general . polish = True | Determine if pilon polishing should be attempted . Do not perform polishing if confindr determines that the sample is contaminated or if there are > 500 contigs | 79 | 35 |
15,794 | def clear_attributes ( self ) : for sample in self . metadata : try : delattr ( sample [ self . analysistype ] , 'record_dict' ) delattr ( sample [ self . analysistype ] , 'contig_lengths' ) delattr ( sample [ self . analysistype ] , 'longest_contig' ) except AttributeError : pass | Remove the record_dict attribute from the object as SeqRecords are not JSON - serializable . Also remove the contig_lengths and longest_contig attributes as they are large lists that make the . json file ugly | 82 | 47 |
15,795 | def run_qaml ( self ) : logging . info ( 'Running GenomeQAML quality assessment' ) qaml_call = 'classify.py -t {tf} -r {rf}' . format ( tf = self . qaml_path , rf = self . qaml_report ) make_path ( self . reportpath ) # Only attempt to assess assemblies if the report doesn't already exist if not os . path . isfile ( self . qaml_report ) : # Run the system calls out , err = run_subprocess ( qaml_call ) # Acquire thread lock, and write the logs to file self . threadlock . acquire ( ) write_to_logfile ( qaml_call , qaml_call , self . logfile ) write_to_logfile ( out , err , self . logfile ) self . threadlock . release ( ) | Create and run the GenomeQAML system call | 191 | 11 |
15,796 | def parse_qaml ( self ) : logging . info ( 'Parsing GenomeQAML outputs' ) # A dictionary to store the parsed excel file in a more readable format nesteddictionary = dict ( ) # Use pandas to read in the CSV file, and convert the pandas data frame to a dictionary (.to_dict()) dictionary = pandas . read_csv ( self . qaml_report ) . to_dict ( ) # Iterate through the dictionary - each header from the CSV file for header in dictionary : # Sample is the primary key, and value is the value of the cell for that primary key + header combination for sample , value in dictionary [ header ] . items ( ) : # Update the dictionary with the new data try : nesteddictionary [ sample ] . update ( { header : value } ) # Create the nested dictionary if it hasn't been created yet except KeyError : nesteddictionary [ sample ] = dict ( ) nesteddictionary [ sample ] . update ( { header : value } ) # Get the results into the metadata object for sample in self . metadata : # Initialise the plasmid extractor genobject setattr ( sample , self . analysistype , GenObject ( ) ) # Initialise the list of all plasmids sample [ self . analysistype ] . prediction = str ( ) # Iterate through the dictionary of results for line in nesteddictionary : # Extract the sample name from the dictionary name = nesteddictionary [ line ] [ 'Sample' ] # Ensure that the names match if name == sample . name : # Append the plasmid name extracted from the dictionary to the list of plasmids sample [ self . analysistype ] . prediction = nesteddictionary [ line ] [ 'Predicted_Class' ] | Parse the GenomeQAML report and populate metadata objects | 373 | 13 |
15,797 | def init ( self , ) : self . gw = None pm = MayaPluginManager . get ( ) genesis = pm . get_plugin ( "Genesis" ) self . GenesisWin = self . subclass_genesis ( genesis . GenesisWin ) | Initialize the plugin . Do nothing . | 52 | 8 |
15,798 | def save_lastfile ( self , tfi ) : tf = models . TaskFile . objects . get ( task = tfi . task , version = tfi . version , releasetype = tfi . releasetype , descriptor = tfi . descriptor , typ = tfi . typ ) c = self . get_config ( ) c [ 'lastfile' ] = tf . pk c . write ( ) | Save the taskfile in the config | 90 | 7 |
15,799 | def stash_calibration ( self , attenuations , freqs , frange , calname ) : self . calibration_vector = attenuations self . calibration_freqs = freqs self . calibration_frange = frange self . calname = calname | Save it for later | 55 | 4 |
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