ó Y_Sc@@s”dZddlmZddlTddlTddlTdZdZi ed 6ed 6e d 6e d 6e d 6e d6e d6e d6e d6Z dd„Zdd„ZdS(s.Sequence IO for NBRF/PIR format. The format is similar to fasta. The header line consistins of '>', a two- letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a sequence ID. The next line is a textual description of the sequence, followed by one or more lines containing the sequence data. The end of the sequence is marked by a "*" (asterisk) character. type_code -- A map between NBRF two letter type codes and Alphabets. see: http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html --- Example NBRF File --- >P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_BOVIN ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK QASGPERTIP ITREEKPAVT AAPKK* i(tabsolute_importi(t*itnbrftpirtalitP1tF1tDLtDCtRCtRLtN3tN1tXXcC@s,gt||ƒD] }|^q}t|ƒS(smRead and parse a NBRF seqquence file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data. If not supplied, then an appropriate alphabet will be inferred from the data. Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable (titerseqtSeqList(tfintalphabettstseqs((s@/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/nbrf_io.pytreadZs "c c@s“tdƒ\}}}|}d }d }d }g} xzt|ƒD]l\} } ||kr×| dks@| jƒrvq@n| ddkrÄ| djdƒ\} }|r®|}n t| }|}q@ntd| ƒ‚q@||krū| jƒ}|}q@q@||kr dj| jƒƒ} | dd kr| j | d ƒt dj| ƒd |jƒd |d |ƒ}|V|}d }d }g} q@q¬| j | ƒq@q@t s@t ‚q@Wd S(sĶ Generate sequences from an NBRF file. arguments: fin -- A stream or file to read alphabet -- yields : Seq raises : ValueError -- On a parse error. itit>it;sParse error on line: %di’’’’Rtnamet descriptionRN( trangetNonet enumeratetisspacetsplitt type_codet ValueErrortstriptjointappendtSeqtFalsetAssertionError(RRtbodytheadertsequencetstatetseq_idtseq_desct seq_alphaRtlinenotlinetseq_typetdatatseq((s@/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/nbrf_io.pyRksJ        N(RR(RRR(t__doc__t __future__RtutilsR2Rtnamest extensionstprotein_alphabett dna_alphabett rna_alphabettgeneric_alphabetRRRR(((s@/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/nbrf_io.pytAs$