ó Y_Sc@@spdZddlmZmZddlTddlTdZd ZdZd d„Z d d „Z d „Z d „Z d S(sÂRead and write a rectangular array of sequence data. One sequence per line and nothing else. Each line must contain the same number of characters. Blank lines and white space are ignored. --- Example Array --- --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD i(tabsolute_importtprint_functioni(t*sé --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD tarraytflatfilecC@s,gt||ƒD] }|^q}t|ƒS(sRead a file of raw sequence alignment 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/array_io.pytread>s "cc@sðt|ƒ}d}x×t|ƒD]É\}}|jƒr=qn|jƒ}|ddkrltd|ƒ‚nt|ƒ}|j|ƒs£td|||fƒ‚n|rÎ|t|ƒkrÎtd|ƒ‚nt|ƒ}t||ƒVqWdS(s/ Read one line of sequence data and yield the sequence. 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 it>sParse Error on input line: %d s.Character on line: %d not in alphabet: %s : %ss%Line %d has an incommensurate length.N( tAlphabett enumeratetisspacetstript ValueErrortremove_whitespacet alphabetictlentSeq(RRt line_lengthtlinenumtline((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/array_io.pyRMs$     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/array_io.pytwriters 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/array_io.pyR}sN(sarrayR((t__doc__t __future__RRRtutilstexampletnamest extensionstNoneR RRR(((sA/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/array_io.pyt*s    %