ó Y_Sc@`s¤dZddlmZmZmZddlZddlTddlTddlTdZ dZ dZ dd„Z dd„Zdd„Zd„Zd„Zdd„ZdS( seRead and write sequence information in FASTA format. This is a very common format for unannotated biological sequence data, accepted by many multiple sequence alignment programs. Each sequence consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. The first word of the description is often the name or ID of the sequence. Fasta files containing multiple sequences have one sequence listed right after another. Example Fasta File :: >Lamprey GLOBIN V - SEA LAMPREY PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------ >Hagfish GLOBIN III - ATLANTIC HAGFISH PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA---------- >Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG ----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH----------- i(tabsolute_importtdivisiontprint_functionNi(t*itfastatpearsontfatfasttseqtfsatfsttnttaatfnatmpfatfaatfnntmfastattfatpfas3 >Lamprey GLOBIN V - SEA LAMPREY PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------ >Hagfish GLOBIN III - ATLANTIC HAGFISH PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA---------- >Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG ----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH----------- cC`sWgt||ƒD] }|^q}td}t|dƒrG|j}nt|d|ƒS(sRead and parse a fasta file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable itname(titerseqtnamesthasattrRtSeqList(tfintalphabettstseqsR((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytreadVs "  cC`stt||ƒƒS(sNRead one sequence from the file, starting from the current file position.(tnextR(RR((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytreadseqgsc c`s6t|ƒ}g}g}d}d}d„}xát|ƒD]Ó\}}|jƒ}|dkrdq:n|jdƒr¾|dk r¥||||||ƒVd}g}n|d}|}g}q:|jdƒrá|j|dƒq:|dkrtd|ƒ‚n|j|ƒq:W|sdS||||||ƒVdS( s' Parse a fasta file and generate sequences. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yeilds: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable iÿÿÿÿcS`sŒy^|jddƒd}|r9|ddj|ƒ7}ntdj|ƒ|d|d|ƒ}Wn'tk r‡td||fƒ‚nX|S( Nt iis tRt descriptionsMParse failed with sequence starting at line %d: Character not in alphabet: %s(tsplittjointSeqt ValueError(RRtheadert header_linenotcommentsRR((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pyt build_seqs( R!t>it;s/Parse failed on line %d: sequence before headerN(tAlphabettNonet enumeratetstript startswithtappendR&( RRRR)R'R(R*tlinenotline((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pyRms8          cC`s\|jr:x.|jjƒD]}td|d|ƒqWnx|D]}t||ƒqAWdS(shWrite a fasta file. Args: fout -- A writable stream. seqs -- A list of Seq's R,tfileN(R"t splitlinestprinttwriteseq(tfoutRR4R((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytwrite¤s   cC`sø|jp|jpd}|rƒ|jƒ}td|dd|ƒt|ƒdkr“x)|dD]}td|d|ƒq_Wq“ntdd|ƒt|ƒ}d}x?td||ƒD])}t||||d|!d|ƒqºWtd|ƒdS( s| Write a single sequence in fasta format. Args: afile -- A writable stream. seq -- A Seq instance R!R+iR5iR,iPN(R"RR6R7tlentrange(tafileRR'thtLt line_lengthtn((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pyR8²s  'c`s=‡fd†}tjdƒ‰‡fd†}t|||ƒS(sbReturn a FileIndex for the fasta file. Sequences can be retrieved by item number or name. c`s t|ˆƒS(N(R(R=(R(sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytparserÏss ^>\s*(\S*)c`s,ˆj|ƒ}|dkrdS|jdƒS(Ni(tsearchR.tgroup(R4tk(tkey(sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytlinekeyÓs (tretcompilet FileIndex(R=RRBRG((RRFsA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pytindexËs(RRsfa(sfaRsfastsseqR R sntR R RRRRRR(t__doc__t __future__RRRRHtutilsRR!Rt extensionstexampleR.RRRR:R8RK(((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/fasta_io.pyt6s       7