ó Y_Sc@`s€dZddlmZmZmZddlTddlTddlTdZdZ d Z dd „Z dd „Z d „Zd „ZdS(s©Read and write sequence information in IntelliGenetics format. A sequence file in IG format can contain several sequences, each consisting of a number of comment lines that must begin with a semicolon (";"), a line with the sequence name and the sequence itself terminated with the termination character '1' for linear or '2' for circular sequences. The termination character is defacto optional. --- Example IG File --- ;H.sapiens fau mRNA, 518 bases HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc actcttaagtcttttgtaattctggctttctctaataaaaaagccactta gttcagtcaaaaaaaaaa1 ;H.sapiens fau 1 gene, 2016 bases HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac accggttctccatccccgcagcgtagcccggaacatggtagctgccatct ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2 i(tabsolute_importtdivisiontprint_functioni(t*itintelligeneticstigtstanfordsû ;H.sapiens fau mRNA, 518 bases HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc actcttaagtcttttgtaattctggctttctctaataaaaaagccactta gttcagtcaaaaaaaaaa1 ;H.sapiens fau 1 gene, 2016 bases HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac accggttctccatccccgcagcgtagcccggaacatggtagctgccatct ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2 cC`s,gt||ƒD] }|^q}t|ƒS(sRead and parse an IG 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 (titerseqtSeqList(tfintalphabettstseqs((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pytreadRs "c c`sot|ƒ}g}g}d}d }d„}xt|ƒD] \}}|jƒ}|dkrdq:n|jdƒr¿|r¥||||||ƒVg}g}d }n|j|dƒ|}q:|sÎ|}q:|ddksî|ddkr4|jt|dd!ƒƒ||||||ƒVg}g}d }q:|jt|ƒƒq:W|rk||||||ƒVnd S( s% Parse an IG 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`sey7dj|ƒ}tdj|ƒ|d|d|ƒ}Wn'tk r`td||fƒ‚nX|S(Ns ttnamet descriptionsMParse failed with sequence starting at line %d: Character not in alphabet: %s(tjointSeqt ValueError(R R RtcommentstlinenotdescR ((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pyt build_seqss( Rt;it1t2iN(tAlphabettNonet enumeratetstript startswithtappendtremove_whitespace( R R R theadert start_linenoRRRtline((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pyRas<         cC`s"x|D]}t||ƒqWdS(s¨Write an IG file. Args: fout -- A writable stream. seqs -- A list of Seq's Raises: ValueError -- If a sequence is missing a name N(twriteseq(tfoutR R ((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pytwrites cC`sÔ|jp d}x(|jƒD]}td|d|ƒqW|js\tdt|ƒƒ‚nt|jd|ƒt|ƒ}d}x?td||ƒD])}t||||d|!d|ƒq–Wtd|ƒdS(sà Write a single sequence in IG format. Args: afile -- A writable stream. seq -- A Seq instance Raises: ValueError -- If a sequence is missing a name RRtfiles+Write failed with missing sequence name: %siPiN(Rt splitlinestprintRRtstrtlentrange(R&tseqRthtLt line_lengthtn((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pyR%ªs   'N(RRR(t__doc__t __future__RRRtutilsR.Rtnamest extensionstexampleRR RR'R%(((sK/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/intelligenetics_io.pyt3s     <