ó Y_Sc@@sRdZddlmZddlTddlTd Zd Zd d„Zd d „Z d S( sTRead GenBank flat files. Currently only reads sequence data and not annotations. i(tabsolute_importi(t*tgenbanktgbtgbkcC@s,gt||ƒD] }|^q}t|ƒS(sRead and parse a file of genbank records. 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((sC/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/genbank_io.pytreads "cc@sÿt|ƒ}g}d„}tt|ƒƒ}xËtrú|j|ƒ}|jdƒsmtd|jƒƒ‚n|jd„ƒ}|jdƒrŸtd|ƒVq0xU|D]M}|jdƒrÜtdj |ƒ|ƒVg}Pn|j |j ƒdƒq¦Wq0WdS( s Iterate over genbank records 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 cS@s t|ƒ S(N(tisblank(tstring((sC/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/genbank_io.pytnotblank6stLOCUSs&Cannot find start of record at line %dcS@s|jdƒp|jdƒS(NtORIGINs//(t startswith(R ((sC/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/genbank_io.pytBss//tiN( tAlphabett ReiteratetitertTruetfilterRt ValueErrortindextSeqtjointextendtsplit(RRtseqRtlinestline((sC/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/genbank_io.pyR%s$    N(R(RRsgbk( t__doc__t __future__RtutilsRtnamest extensionstNoneR R(((sC/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/genbank_io.pyts