[BioPython] Blast Parser

[Jeffrey Chang]

Try using the latest version of NCBIStandalone from cvs.biopython.org.  
If it still doesn't work, please email me the blast run that is causing 
the problem.

Jeff


On Thursday, June 12, 2003, at 04:06  AM, Emmanuel TALLA wrote:

> Hi everyone,
>
> I'm trying to parse a blast file with the NCBIStandalone module and I 
> get
> the following error messages. The Blast file is done with Blast 2.2.5 
> or
> 2.2.6. What wrong with the blast parsing???
>
> Thanks
>
> Emmanuel
>
> ###### Error messages
> File "./test_parsing_blast.py", line 56, in ?
>     print BlastParser2CrossHyb()
>   File "./test_parsing_blast.py", line 16, in BlastParser2CrossHyb
>     b_record = b_iterator.next()
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 1353, in next
>     return self._parser.parse(File.StringHandle(data))
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 515, in parse
>     self._scanner.feed(handle, self._consumer)
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 84, in feed
>     self._scan_rounds(uhandle, consumer)
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 140, in _scan_rounds
>     self._scan_alignments(uhandle, consumer)
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 261, in _scan_alignments
>     self._scan_masterslave_alignment(uhandle, consumer)
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 364, in _scan_masterslave_alignment
>     consumer.multalign(line)
>   File 
> "/local/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py",
> line 769, in multalign
>     name = string.rstrip(line[:self._name_length])
> TypeError: sequence index must be integer
>
>
> ############# The parser script ##################
> #! /local/bin/python
> from string import *
> from Bio.Blast import NCBIStandalone
>
>
> def BlastParser2CrossHyb():
>     BlastFile = "YBR301w.dna.bln"
>     blast_out = open(BlastFile,'r')
>     b_parser = NCBIStandalone.BlastParser()
>     b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
>
>     ID_threshold = 40
>     ML_threshold = 25
>     LC_threshold = 20
>     ListeCH=[]
>
>     while 1:
>         b_record = b_iterator.next()
>
>         if b_record is None:
>             break
>
>         for hit in b_record.alignments:
>             for hsp in hit.hsps:
>                 tupleId = hsp.identities#renvoi un tuple
>                 Id = float(tupleId[0])
>                 ML= tupleId[1]
>                 ID= 100*Id/ML
>                 matches = hsp.match
>                 Lmatch = matches.split()
>                 Lmatch.sort()
>                 Lmatch.reverse()
>                 LC = len(Lmatch[0])
>                 if (ML >= ML_threshold and ID >= ID_threshold) or (LC 
> >=
> LC_threshold):
>                     tupleGap = hsp.gaps # renvoi  un tuple
>                     gap = tupleGap[0]
>                     if gap == None:
>                         gap = 0
>
>                     QueryStart = hsp.query_start
>                     QueryEnd = hsp.query_start + ML - 1 - gap
> 			
>                     tupleStrand = hsp.strand
>                     if tupleStrand[1] == 'Minus':
>                         SubjectStart = hsp.sbjct_start - ML + 1 
> #question
> gap sur le subject???
>                         SubjectEnd = hsp.sbjct_start
>                     else:
>                         SubjectStart = hsp.sbjct_start
>                         SubjectEnd = hsp.sbjct_start + ML - 1 #ne 
> tient pas
> compte du gap
>
>                     key = [QueryStart, QueryEnd, hit.title[1:],
> SubjectStart, SubjectEnd, ID, tupleStrand[1]]
>                     ListeCH.append(key)
>
>     blast_out.close()
>     return ListeCH
>
>
> print BlastParser2CrossHyb()
>
> ############
> **************************************
> Emmanuel TALLA, Ph.D
> Institut Pasteur
> Genetique Moleculaire des levures
> 25, rue du dr Roux
> 75724 Paris cedex 15
> France
> Tel: +33(0)1.40.61.30.59
> Fax: +33(0)1.40.61.34.56
> ****************************************
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