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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Oct 13 10:59:11 UTC 2009


------- 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)
for b_round in b_record.rounds :
    print "Round %i has %i alignments" \
          % (b_round.number, len(b_round.alignments))


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:


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