* D;c s`dZdkTdkZdkZdgZ$dklZ%dklZ&dklZ'dkl Z (dk T)dkl Z +d fd YZ Gd fd YZ td fdYZdefdYZdfdYZdfdYZdefdYZdefdYZ8edZdS(sFasta package This module provides code to work with FASTA-formatted sequences. Classes: Record Holds FASTA sequence data. Iterator Iterates over sequence data in a FASTA file. Dictionary Accesses a FASTA file using a dictionary interface. RecordParser Parses FASTA sequence data into a Record object. SequenceParser Parses FASTA sequence data into a Sequence object. _Scanner Scans a FASTA-format stream. _RecordConsumer Consumes FASTA data to a Record object. _SequenceConsumer Consumes FASTA data to a Sequence object. Functions: index_file Index a FASTA file for a Dictionary. (s*Ns FastaAlign(sFile(sIndex(sSeq(s SeqRecord(sAlphabetsRecordcs)+dZ23ddZ>dZRS(sHolds information from a FASTA record. Members: title Title line ('>' character not included). sequence The sequence. i<cs.39:d|_;d|_<||_dS(s__init__(self, colwidth=60) Create a new Record. colwidth specifies the number of residues to put on each line when generating FASTA format. sN(sselfstitlessequencescolwidths _colwidth(sselfscolwidth((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__3s  cs>?g}@|id|iAd}BxOB|t|ijo5C|i|i|||i!D||i}q2WEti |dSdS(Ns>%sis ( sssappendsselfstitlesislenssequences _colwidthsstringsjoin(sselfsssi((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__str__>s  !(s__doc__s__init__s__str__(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysRecord+s  sIteratorcs)GdZMNedZ[dZRS(sReturns one record at a time from a FASTA file. Methods: next Return the next record from the stream, or None. csdNUVt|tj ot|tj oWtdnXti||_Y||_ dS(s__init__(self, handle, parser=None) Create a new iterator. handle is a file-like object. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. s,I expected a file handle or file-like objectN( stypeshandlesFileTypes InstanceTypes ValueErrorsFiles UndoHandlesselfs_uhandlesparsers_parser(sselfshandlesparser((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__Ns )cs[abg}cxzcdood|ii}e| ofPng|ddjo|oh|ii|iPnj|i|qWl| o mtSnoti |d}p|i tj o q|i i t i|Snr|SdS(s}next(self) -> object Return the next FASTA record from the file. If no more records, return None. iis>sN(slinessselfs_uhandlesreadlineslinessavelinesappendsNonesstringsjoinsdatas_parsersparsesFiles StringHandle(sselfsdataslinessline((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysnext[s"      (s__doc__sNones__init__snext(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysIteratorGs  s DictionarycsVtdZwxdZzedZdZdZdZdZRS(s9Accesses a FASTA file using a dictionary interface. s __filenamecsGzti||_t|iti|_||_ dS(s__init__(self, indexname, parser=None) Open a Fasta Dictionary. indexname is the name of the index for the dictionary. The index should have been created using the index_file function. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. N( sIndexs indexnamesselfs_indexsopens Dictionarys_Dictionary__filename_keys_handlesparsers_parser(sselfs indexnamesparser((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__zs cst|iSdS(N(slensselfs_index(sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__len__scs|i|\}}|ii||ii|}|i t j o |i i t i |Sn|SdS(N(sselfs_indexskeysstartslens_handlesseeksreadsdatas_parsersNonesparsesFiles StringHandle(sselfskeyslensdatasstart((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys __getitem__s  cst|i|SdS(N(sgetattrsselfs_indexsname(sselfsname((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys __getattr__scs|ii}g}x;|dr.}|d djo|i|nq-Wx#|dr}|i|qnW|SdS(sOverride keys to return only valid keys. The keys which is called normally on this dictionary will return internal values such as '__filename'. This just strips those out before returning. iis__N(sselfs_indexskeyssall_keyss to_removeskeysappendsremove(sselfskeys to_removesall_keys((s+/mit/seven/lib/python/Bio/Fasta/__init__.pyskeyss   (s__doc__s_Dictionary__filename_keysNones__init__s__len__s __getitem__s __getattr__skeys(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys Dictionaryts     s RecordParsercs&dZdZdZRS(s6Parses FASTA sequence data into a Record object. cs%t|_t|_dS(N(s_Scannersselfs_scanners_RecordConsumers _consumer(sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__scs-|ii||i|iiSdS(N(sselfs_scannersfeedshandles _consumersdata(sselfshandle((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysparses(s__doc__s__init__sparse(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys RecordParsers  sSequenceParsercs/dZeiedZdZRS(s8Parses FASTA sequence data into a Sequence object. cs.t|_t|||_dS(sInitialize a Scanner and Sequence Consumer. Arguments: o alphabet - The alphabet of the sequences to be parsed. If not passed, this will be set as generic_alphabet. o title2ids - A function that, when given the title of the FASTA file (without the beginning >), will return the name, id and description (in that order) for the record. If this is not given, then the entire title line will be used as the description. N(s_Scannersselfs_scanners_SequenceConsumersalphabets title2idss _consumer(sselfsalphabets title2ids((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__s cs-|ii||i|iiSdS(N(sselfs_scannersfeedshandles _consumersdata(sselfshandle((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysparses(s__doc__sAlphabetsgeneric_alphabetsNones__init__sparse(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysSequenceParsers s_Scannercs>dZdZdZdZdZRS(sVScans a FASTA-formatted file. Methods: feed Feed in one FASTA record. csft|tio |}nti|}|io|i||ndS(sfeed(self, handle, consumer) Feed in FASTA data for scanning. handle is a file-like object containing FASTA data. consumer is a Consumer object that will receive events as the FASTA data is scanned. N( s isinstanceshandlesFiles UndoHandlesuhandlespeeklinesselfs _scan_recordsconsumer(sselfshandlesconsumersuhandle((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysfeeds  csG|i|i|||i|||idS(N(sconsumersstart_sequencesselfs _scan_titlesuhandles_scan_sequences end_sequence(sselfsuhandlesconsumer((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys _scan_records cs t||idddS(Nsstarts>(s read_and_callsuhandlesconsumerstitle(sselfsuhandlesconsumer((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys _scan_titlescsxrdog|i}t|oPn-|ddjo|i|Pn|i|q WdS(Niis>(suhandlesreadlineslines is_blank_linessavelinesconsumerssequence(sselfsuhandlesconsumersline((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys_scan_sequences (s__doc__sfeeds _scan_records _scan_titles_scan_sequence(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys_Scanners    s_RecordConsumercsJdZdZdZdZdZ dZRS(suConsumer that converts a FASTA record to a Record object. Members: data Record with FASTA data. cst|_dS(N(sNonesselfsdata(sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__scst|_dS(N(sRecordsselfsdata(sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysstart_sequencescs dS(N((sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys end_sequencescsEto|ddjptti|d|i_dS(Nis>i(s __debug__slinesAssertionErrorsstringsrstripsselfsdatastitle(sselfsline((s+/mit/seven/lib/python/Bio/Fasta/__init__.pystitles"cs2  ti|} |ii||i_dS(N(sstringsrstripslinesseqsselfsdatassequence(sselfslinesseq((s+/mit/seven/lib/python/Bio/Fasta/__init__.pyssequence s(s__doc__s__init__sstart_sequences end_sequencestitlessequence(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys_RecordConsumers     s_SequenceConsumercsSdZeiedZ"dZ&dZ)dZ3dZRS(suConsumer that converts a FASTA record to a Sequence object. Members: data Sequence with FASTA data. cs.t|_||_ ||_dS(sInitialize the Consumer. Arguments: o alphabet - The alphabet of the sequences we will be creating. o title2ids - A function that will convert the title of a FASTA record into the id, name and description information. N(sNonesselfsdatasalphabets title2ids(sselfsalphabets title2ids((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys__init__s  cs4"#tid|i}$ti||_dS(Ns(sSeqsselfsalphabetsseqs SeqRecordsdata(sselfsseq((s+/mit/seven/lib/python/Bio/Fasta/__init__.pysstart_sequence"scs &'dS(N((sself((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys end_sequence&scs)*to|ddjpt+|ioY,|iti|d\}}}-||i _.||i _/||i _ n1ti|d|i _ dS(Nis>i( s __debug__slinesAssertionErrorsselfs title2idssstringsrstripsidsnamesdescrsdatas description(sselfslinesidsdescrsname((s+/mit/seven/lib/python/Bio/Fasta/__init__.pystitle)s" (csA35titi||i}6|ii||i_dS(N(sSeqsstringsrstripslinesselfsalphabetsseqsdata(sselfslinesseq((s+/mit/seven/lib/python/Bio/Fasta/__init__.pyssequence3s!( s__doc__sAlphabetsgeneric_alphabetsNones__init__sstart_sequences end_sequencestitlessequence(((s+/mit/seven/lib/python/Bio/Fasta/__init__.pys_SequenceConsumers    c sc8ABtii| oCtd|nEti|dd}F||ti <Ht t |dt }IxIdoJ|ii}K|i}L|ii|}N|tjoOPnP|tj oQ||}n S|i}U| oVtdn(W|i|oXtd|nZ||f||