o Rŀg7@sDdZddlZddlZddlmZddlmZddlmZddlm Z ddlm Z ddlm Z dd lm Z d d l mZd d lmZd ZdeZdZdZdeZdeZGdddZGdddeZeZGdddZGdddZGdddZGdddeZGdddeZdd Z d!d"Z!e"d#krdd$l#m$Z$e$dSdS)%a 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) N)BiopythonParserWarning)Seq)Location)LocationParserError) Reference) SeqFeature)SimpleLocation)GenBankScanner)FeatureValueCleaner  c@s*eZdZdZd ddZddZddZdS) Iteratora<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. NcCs||_||_dS)aInitialize 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. N)handle_parser)selfrparserrH/var/www/html/myenv/lib/python3.10/site-packages/Bio/GenBank/__init__.py__init__Is zIterator.__init__cCsl|jdur#g} |j}|sdS|||dkrnqd|Sz|j|jWSty5YdSw)zlReturn the next GenBank record from the handle. Will return None if we ran out of records. NTz//)rrreadlineappendrstripjoinparse StopIteration)rlineslinerrr__next__Us      zIterator.__next__cCs t|jdS)zIterate over the records.N)iterr!rrrr__iter__i zIterator.__iter__N)__name__ __module__ __qualname____doc__rr!r$rrrrrAs   rc@seZdZdZdS)ParserFailureErrorz5Failure caused by some kind of problem in the parser.N)r'r(r)r*rrrrr+nsr+c@s"eZdZdZd ddZddZdS) FeatureParserzParse 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. rr NcCs(t||_||_|r||_dSt|_dS)aInitialize 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. N)r _scanner use_fuzziness_cleaner)r debug_levelr.feature_cleanerrrrr~s   zFeatureParser.__init__cCs"t|j|j}|j|||jS)zParse the specified handle.)_FeatureConsumerr.r/r-feeddatarr _consumerrrrrszFeatureParser.parse)rr Nr'r(r)r*rrrrrrr,us  r,c@s"eZdZdZdddZddZdS) RecordParserzParse 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. rcCt||_dS)ajInitialize 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. N)r r-)rr0rrrr zRecordParser.__init__cCst}|j|||jS)z1Parse the specified handle into a GenBank record.)_RecordConsumerr-r3r4r5rrrrszRecordParser.parseN)rr7rrrrr8s r8c@s~eZdZdZdgZddZeddZeddZed d Z ed d Z ed dZ eddZ eddZ eddZdS)_BaseGenBankConsumerzAbstract GenBank consumer providing useful general functions (PRIVATE). This just helps to eliminate some duplication in things that most GenBank consumers want to do. translationcCdSr&rr#rrrrz_BaseGenBankConsumer.__init__cCsL|dks|dkr d}n|ddkr|dd}n|}|d}dd|DS)zz8_BaseGenBankConsumer._split_keywords..)split)keyword_stringkeywords keyword_listrrr_split_keywordss  z$_BaseGenBankConsumer._split_keywordscCs&|dddd}dd|DS)z:Split a string of accession numbers into a list (PRIVATE). r rBcSsg|] }|r|qSrrDrFrrrrIsz:_BaseGenBankConsumer._split_accessions..)replacerK)accession_string accessionrrr_split_accessionssz&_BaseGenBankConsumer._split_accessionscCs|r|dkrgS|ddkr|dd}n|}|d}g}|D] }|d}||q d|vr:|dd|vs1dd|DS) z8Split a string with taxonomy info into a list (PRIVATE).r@rANrBrPrcSrCrrDrFrrrrIrJz8_BaseGenBankConsumer._split_taxonomy..)rKextendremove)taxonomy_stringtax_infotax_list new_tax_listtax_item new_itemsrrr_split_taxonomys      z$_BaseGenBankConsumer._split_taxonomycCsd|S)zClean whitespace out of a location string (PRIVATE). The location parser isn't a fan of whitespace, so we clean it out before feeding it into the parser. rrrK)location_stringrrr_clean_locationr:z$_BaseGenBankConsumer._clean_locationcCs"ddg}|D]}||d}q|S)zKRemove any newlines in the passed text, returning the new string (PRIVATE).rP rrQ)textnewlineswsrrr_remove_newlinessz%_BaseGenBankConsumer._remove_newlinescCsddd|dDS)zHReplace multiple spaces in the passed text with single spaces (PRIVATE).r cs|]}|r|VqdSr&rrFrrr z9_BaseGenBankConsumer._normalize_spaces..r^rcrrr_normalize_spaces sz&_BaseGenBankConsumer._normalize_spacescCs |ddS)z1Remove all spaces from the passed text (PRIVATE).r rrbrjrrr_remove_spacess z#_BaseGenBankConsumer._remove_spacescCs|d}|}||fS)aConvert 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. r r)startend new_startnew_endrrr_convert_to_python_numberssz/_BaseGenBankConsumer._convert_to_python_numbersN)r'r(r)r*remove_space_keysr staticmethodrOrTr]r`rfrkrlrqrrrrr<s(        r<c@seZdZdZdkddZddZddZd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZddZddZddZdd Zd!d"Zd#d$Zd%d&Zd'd(Zd)d*Zd+d,Zd-d.Zd/d0Zd1d2Zd3d4Zd5d6Zd7d8Zd9d:Zd;d<Z d=d>Z!d?d@Z"dAdBZ#dCdDZ$dEdFZ%dGdHZ&dIdJZ'dKdLZ(dMdNZ)dOdPZ*dQdRZ+dSdTZ,dUdVZ-dWdXZ.dYdZZ/d[d\Z0d]d^Z1d_d`Z2dadbZ3dcddZ4dedfZ5dgdhZ6didjZ7dS)lr2a&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. NcCsbddlm}t||ddd|_d|j_d|j_||_||_d|_ g|_ d|_ d|_ d|_ dS)Nr) SeqRecord)idr) Bio.SeqRecordrtr<rr4ru description_use_fuzziness_feature_cleaner _seq_type _seq_data_cur_reference _cur_feature_expected_size)rr.r1rtrrrr4s   z_FeatureConsumer.__init__cCs ||j_dS)z6Set the locus name is set as the name of the Sequence.N)r4name)r locus_namerrrlocusEr%z_FeatureConsumer.locuscCr9)zRecord the sequence length.N)intr~rcontentrrrsizeIsz_FeatureConsumer.sizecCs||_dS)zRecord 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. N)rErz)rtyperrr residue_typeMsz_FeatureConsumer.residue_typecCs0|r|dvrtd|d||jjd<dSdS)yValidate and record sequence topology. The topology argument should be "linear" or "circular" (string). linearcircularUnexpected topology  should be linear or circulartopologyN)r+r4 annotationsrrrrrrVs z_FeatureConsumer.topologycCsn|r5d|vs d|vrtd|d|dddvr-|dds-td|t||jjd <dSdS) ;Validate and record the molecule type (for round-trip etc).rrMolecule type  should not include topologyNDNARNA,Non-upper case molecule type in LOCUS line: molecule_type)r+upperisupperwarningswarnrr4rrmol_typerrrrbs $ z_FeatureConsumer.molecule_typecC||jjd<dS)Ndata_file_divisionr4r)rdivisionrrrrwz#_FeatureConsumer.data_file_divisioncCr)Ndater)r submit_daterrrrzrz_FeatureConsumer.datecC,|jjr|jjd|7_dS||j_dS)z6Set the definition as the description of the sequence.r N)r4rw)r definitionrrrr}s z_FeatureConsumer.definitioncCs||}z|D]}||jjdvr|jjd|qWnty,||jjd<Ynw|jjsCt|dkrE|jjdd|j_dSdSdS)zSet the accession number as the id of the sequence. If we have multiple accession numbers, the first one passed is used. accessionsrN)rTr4rrKeyErrorrulen)racc_num new_acc_numsaccrrrrSs   z_FeatureConsumer.accessioncC|d|jjd<dS)N-tlsrKr4rrrrrrz_FeatureConsumer.tlscCr)Nrtsarrrrrrrz_FeatureConsumer.tsacCr)Nrwgsrrrrrrrz_FeatureConsumer.wgscCs |jjdg|ddS)N wgs_scafldr)r4r setdefaultrrKrrrradd_wgs_scafld z_FeatureConsumer.add_wgs_scafldcCr)Nnidrrrrrrrz_FeatureConsumer.nidcCr)Npidrrrrrrrz_FeatureConsumer.pidcCs`|ddkr&|ddr&||dd||dddS|r.||j_dSdS)Nr@r r)countrKisdigitrSversion_suffixr4ru)r version_idrrrversions  z_FeatureConsumer.versioncCs,|dd}|jjdd|DdS)aHandle 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. zGenomeProject:zProject:csrgr&rrGprrrrhriz+_FeatureConsumer.project..N)rQr4dbxrefsrUrKrrrrprojects  z_FeatureConsumer.projectcCsFd|vr|dd}d|vs||jjvr!|jj|dSdS)aStore 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 z: :N)rQrEr4rrrrrrdblinks  z_FeatureConsumer.dblinkcCs |sJt||jjd<dS)zSet 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. sequence_versionN)rrr4r)rrrrrrs z_FeatureConsumer.version_suffixcCs||jjd<dS)N db_source)rr4rrrrrrsz_FeatureConsumer.db_sourcecCr)Ngirrrrrr rz_FeatureConsumer.gicCs>d|jjvr|jjd||dS|||jjd<dS)NrM)r4rrUrOrrrrrM s z_FeatureConsumer.keywordscCr)Nsegmentrrrrrrrz_FeatureConsumer.segmentcCs<|dkrd}n|ddkr|dd}n|}||jjd<dS)NrrAr@sourcer)rr source_inforrrrs  z_FeatureConsumer.sourcecCr)Norganismrrrrrr"rz_FeatureConsumer.organismcCsD||}z |jjd|WdSty!||jjd<YdSw)z.Record (another line of) the taxonomy lineage.taxonomyN)r]r4rrUr)rrlineagerrrr%s  z_FeatureConsumer.taxonomycCs8|jdur|jjd|jng|jjd<t|_dS)z/Signal the beginning of a new reference object.N references)r|r4rrrrrrr reference_num-s   z_FeatureConsumer.reference_numcCs|ds J||dd}g}d|vr*d|vr*|dd}||}||n9d|vrLd|vrL|d}||td d}||}||n|d ksV|dkrWn td |d |jj||j _ dS) aAttempt 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) )r rAbasestorNresiduesz residues siteszCould not parse base info z in record ) endswith_split_reference_locationsrUfindrrE ValueErrorr4rur|location)rr ref_base_info all_locations locationsresidues_startrrrreference_bases8s$        z _FeatureConsumer.reference_basesc Cs^|d}g}|D]#}|d\}}|t|t|\}}t||} || q |S)a!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. rBr)rKrqrrErr) rr_ all_base_info new_locations base_informrnrorp this_locationrrrr`s   z+_FeatureConsumer._split_reference_locationscC,|jjr|jjd|7_dS||j_dSNr r|authorsrrrrrw z_FeatureConsumer.authorscCrrr|consrtmrrrrr}rz_FeatureConsumer.consrtmcCsF|jdur tdtdS|jjr|jjd|7_dS||j_dS)N*GenBank TITLE line without REFERENCE line.r r|rrrtitlerrrrrs  z_FeatureConsumer.titlecCrrr|journalrrrrrrz_FeatureConsumer.journalcC ||j_dSr&r| medline_idrrrrr z_FeatureConsumer.medline_idcCrr&r| pubmed_idrrrrrrz_FeatureConsumer.pubmed_idcCr)zDeal with a reference comment.r N)r|commentrrrrremarks z_FeatureConsumer.remarkcCsLz|jjddd|7<WdSty%d||jjd<YdSw)NrrP)r4rrrrrrrrs $ z_FeatureConsumer.commentcCr)Nstructured_commentrrrrrrrz#_FeatureConsumer.structured_commentcC |dSz?Get ready for the feature table when we reach the FEATURE line.Nstart_feature_tablerrrr features_liner%z_FeatureConsumer.features_linecCs,|jdur|jjd|jd|_dSdS)z5Indicate we've got to the start of the feature table.Nr)r|r4rrr#rrrrs  z$_FeatureConsumer.start_feature_tablecCs$t|_||j_|jj|jdSr&)rr}rr4featuresrrrrr feature_keysz_FeatureConsumer.feature_keyc Cs||}d|vr|d}|d|}|j}d|jjddv}d|jv}z t ||||}Wnt yQ}zt |dtd }WYd }~nd }~ww||j_d S) zParse 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. rQ,rrrPROTEINz#; setting feature location to None.N)r`rr~r4rgetlowerrzrr fromstringrrrrr}r) rr location_line comma_poslength is_circularstrandedrerrrrs"     z_FeatureConsumer.locationcCs|dur||jjvrdg|jj|<dSdSt|dkr-|ddkr-|ddkr-|dd}td|r;td|t|d d}|j durM|j ||}||jjvr^|jj| |dS|g|jj|<dS) zWhen we get a qualifier key and its value. Can receive None, since you can have valueless keys such as /pseudo Nrr r"rAz[^"]"[^"]|^"[^"]|[^"]"$zuThe NCBI states double-quote characters like " should be escaped as "" (two double - quotes), but here it was not: %rz"") r} qualifiersrresearchrrrrQry clean_valuerrkeyvaluerrrfeature_qualifiers( $     z"_FeatureConsumer.feature_qualifiercCtdz)Use feature_qualifier instead (OBSOLETE).z)Use the feature_qualifier method instead.NotImplementedError)r content_listrrrfeature_qualifier_namez'_FeatureConsumer.feature_qualifier_namecCrrrrrrrfeature_qualifier_descriptionrz._FeatureConsumer.feature_qualifier_descriptioncCs||jjd<dS)zDeal with CONTIG information.contigNrrrrrcontig_location sz _FeatureConsumer.contig_locationcCr>r&rrrrr origin_namer?z_FeatureConsumer.origin_namecCr>r&rrrrr base_count r?z_FeatureConsumer.base_countcCr>r&rrrrr base_number#r?z_FeatureConsumer.base_numbercC d|vsJ|j|dS)zAdd 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 r Nr{rrrrrrsequence&s z_FeatureConsumer.sequencecCs|jjsd|jjvrtdt|jjd|jj|j_n#|jjddkr@z|jjd|jjd7_Wn ty?Ynwd|j }|j durht |dkrh|j t |krht d |j t ||jjftd}|jrd |jvs{d |jvr~d }n'd |jvrd }nd |jvs|jdkrd}n|jdvrntd|j|dur|jjd||jjd<|s|j rtd|j d|j_dSt||j_dS)z(Clean up when we've finished the record.rz,Problem adding version number to accession: r@rz.%irrNz+Expected sequence length %i, found %i (%s).rMRNArrPRTprotein)rr unspecifiedz/Could not determine molecule_type for seq_type r)r )r4rurrstrrrrrr{r~rrrrrzrrrseq)rrr%rrrr record_end0sX         z_FeatureConsumer.record_endr&)8r'r(r)r*rrrrrrrrrrSrrrrrrrrrrrrrMrrrrrrrrrrrrrrrrrrrrrrrrr r!r"r%r,rrrrr2)sl     !  ( !' r2c@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZddZddZd d!Zd"d#Zd$d%Zd&d'Zd(d)Zd*d+Zd,d-Zd.d/Zd0d1Zd2d3Zd4d5Zd6d7Zd8d9Zd:d;Z dd?Z"d@dAZ#dBdCZ$dDdEZ%dFdGZ&dHdIZ'dJdKZ(dLdMZ)dNdOZ*dPdQZ+dRdSZ,dTdUZ-dVdWZ.dXdYZ/dZd[Z0d\d]Z1d^d_Z2d`daZ3dbdcZ4dddeZ5dfdgZ6dhdiZ7djS)kr;zLCreate a GenBank Record object from scanner generated information (PRIVATE).cCs<t|ddlm}||_g|_d|_d|_d|_dS)Nr Record) r<rrr.r4r{r|r}_cur_qualifier)rr.rrrrts    z_RecordConsumer.__init__cC|d|j_dSNr)rKr4rrrrrrz_RecordConsumer.tlscCr0r1)rKr4rrrrrrr2z_RecordConsumer.tsacCr0r1)rKr4rrrrrrr2z_RecordConsumer.wgscCs|jj|ddSr1)r4rrrKrrrrrsz_RecordConsumer.add_wgs_scafldcCrr&)r4rrrrrrrz_RecordConsumer.locuscCrr&)r4rrrrrrrz_RecordConsumer.sizecCs0d|vsd|vrtd|dt||j_dS)NdnarnazInvalid seq_type (z): DNA/RNA should be uppercase.)rrrr4rrrrrrs   z_RecordConsumer.residue_typecCrr&)r4rrrrrrrz"_RecordConsumer.data_file_divisioncCrr&)r4rrrrrrrz_RecordConsumer.datecCrr&)r4rrrrrrrz_RecordConsumer.definitioncCs.||D]}||jjvr|jj|qdSr&)rTr4rSr)rrrrrrrSs  z_RecordConsumer.accessioncCsj|r3d|vs d|vrtd|d|dddvr-|dds-td|t||j_dSdS) rrrrrrNrr)r+rrrrrr4rrrrrrs $  z_RecordConsumer.molecule_typecCs,|r|dvrtd|d||j_dSdS)rrrrN)r+r4rrrrrrs  z_RecordConsumer.topologycCrr&)r4rrrrrrrz_RecordConsumer.nidcCrr&)r4rrrrrrrz_RecordConsumer.pidcCrr&)r4rrrrrrrz_RecordConsumer.versioncCs||j_dSr&)rr4rrrrrrrz_RecordConsumer.db_sourcecCrr&)r4rrrrrrrz_RecordConsumer.gicC|||j_dSr&)rOr4rMrrrrrMr2z_RecordConsumer.keywordscCs |jjdd|DdS)Ncsrgr&rrrrrrhriz*_RecordConsumer.project..)r4projectsrUrKrrrrrrz_RecordConsumer.projectcCs|jj|dSr&)r4dblinksrrrrrrr2z_RecordConsumer.dblinkcCrr&)r4rrrrrrrz_RecordConsumer.segmentcCrr&)r4rrrrrrrz_RecordConsumer.sourcecCrr&)r4rrrrrrrz_RecordConsumer.organismcCr5r&)r]r4rrrrrrr2z_RecordConsumer.taxonomycCs<|jdur |jj|jddlm}||_||j_dS)zBGrab the reference number and signal the start of a new reference.Nr r-)r|r4rrrr.rnumberrrr.rrrrs    z_RecordConsumer.reference_numcCrr&)r|rrrrrrrz_RecordConsumer.reference_basescCrr&rrrrrrrz_RecordConsumer.authorscCrr&rrrrrrrz_RecordConsumer.consrtmcCs&|jdur tdtdS||j_dS)Nrrrrrrrs  z_RecordConsumer.titlecCrr&rrrrrr rz_RecordConsumer.journalcCrr&rrrrrr rz_RecordConsumer.medline_idcCrr&rrrrrrrz_RecordConsumer.pubmed_idcCrr&)r|rrrrrrrz_RecordConsumer.remarkcCs|jjd|7_dS)NrP)r4rrrrrrrsz_RecordConsumer.commentcCrr&)r4rrrrrrrz"_RecordConsumer.structured_commentcCs|jj|dS)z)Save reference data for the PRIMARY line.N)r4primaryrrrrrprimary_ref_linez _RecordConsumer.primary_ref_linecCr>r&rrrrrr:r?z_RecordConsumer.primarycCrrrrrrrr"r%z_RecordConsumer.features_linecCs"|jdur|jj|jdSdS)z&Signal the start of the feature table.N)r|r4rrr#rrrr&s z#_RecordConsumer.start_feature_tablecCs*|ddlm}||_||j_dS)zBGrab the key of the feature and signal the start of a new feature.r r-N) _add_featurerr.Featurer}rr9rrrr,s   z_RecordConsumer.feature_keycCsB|jdur|jdur|jj|jd|_|jj|jdSdS)zAdd 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. N)r}r/rrr4rr#rrrr=6s  z_RecordConsumer._add_featurecCr5r&)r`r}rrrrrrFr2z_RecordConsumer.locationcCs&||g|dur||dSdSr&)rrrrrrrIs z!_RecordConsumer.feature_qualifiercCsZddlm}|D]"}|dsd|}|jdur!|jj|j||_||j_qdS)zDeal 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) r r-/N) rr. startswithr/r}rr Qualifierr)rrr.rrrrrNs      z&_RecordConsumer.feature_qualifier_namecCs^d|jjvr|jjd|j_||}|jjD] }||jjvr%||}q|||j_dS)N=)r/rrf __class__rrrlrkr)rr cur_contentremove_space_keyrrrrbs     z-_RecordConsumer.feature_qualifier_descriptioncCrr&)r4 base_countsrrrrr!nrz_RecordConsumer.base_countcCrr&)r4originrrrrr qrz_RecordConsumer.origin_namecCs|||j_dS)z>> 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. )r"rr8)rrrrrs rcCsTt|}zt|}Wn tytddwzt|tdty)Y|Sw)aORead 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. zNo records found in handleNz$More than one record found in handle)rnextrr)riteratorrecordrrrreads     rK__main__) run_doctest)%r*rrBiorBio.SeqrBio.SeqFeaturerrrrrScannerr utilsr GENBANK_INDENTGENBANK_SPACERFEATURE_KEY_INDENTFEATURE_QUALIFIER_INDENTFEATURE_KEY_SPACERFEATURE_QUALIFIER_SPACERrrr+r/r,r8r<r2r;rrKr' Bio._utilsrMrrrrsL          -'oL