[Biopython-dev] [Bug 2927] Problem parsing PSI-BLAST plain text output with NCBStandalone.PSIBlastParser

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2927





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-10-13 06:59 EST -------
I have tried parsing your sample output, and it seems fine:

from Bio.Blast.NCBIStandalone import PSIBlastParser
b_parser = PSIBlastParser()
handle = open("Q3V4Q0.psiblast.txt")
b_record = b_parser.parse(handle)
handle.close()
for b_round in b_record.rounds :
    print "Round %i has %i alignments" \
          % (b_round.number, len(b_round.alignments))


Gives:

Round 1 has 385 alignments
Round 2 has 1000 alignments
Round 3 has 1000 alignments
Round 4 has 1000 alignments
Round 5 has 1000 alignments

I don't think the real problem is in the parser, but I will reply with more
details on the mailing list:
http://lists.open-bio.org/pipermail/biopython/2009-October/005660.html

Peter


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