σ Y_Sc@@svdZddlmZmZddlTddlmZdZdZdZ d d „Z d d „Z d „Z d „Zd S(s€Read and write raw, unformatted sequence data. The whole file is read in as a sequence. Whitespace is removed. --- Example Plain/Raw/Text File --- --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD i(tabsolute_importtprint_functioni(t*(tremove_whitespacesΛ --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIV tplaintrawcC@s,gt||ƒD] }|^q}t|ƒS(s Read a file of raw sequence data. 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((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/plain_io.pytread=s "cc@sΟt|ƒ}g}xŸt|ƒD]‘\}}|jƒr=qn|jƒ}|ddkrltd|ƒ‚nt|ƒ}|j|ƒs£td|||fƒ‚n|j|ƒqWtdj |ƒ|ƒVdS(s6 Read the sequence data and yield one (and only one) sequence. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable it>sParse Error on input line: %d s.Character on line: %d not in alphabet: %s : %stN( tAlphabett enumeratetisspacetstript ValueErrorRt alphabetictappendtSeqtjoin(RR tlinestlinenumtline((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/plain_io.pyRLs    cC@s"x|D]}t||ƒqWdS(s‰Write raw sequence data, one line per sequence. arguments: afile -- A writable stream. seqs -- A list of Seq's N(twriteseq(tafileR R ((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/plain_io.pytwritens cC@st|d|ƒdS(s Write a single sequence in raw format. arguments: afile -- A writable stream. seq -- A Seq instance tfileN(tprint(Rtseq((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/plain_io.pyRysN(splainsraw((t__doc__t __future__RRR tutilsRtexampletnamest extensionstNoneR RRR(((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/plain_io.pyt)s    "