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

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





------- Comment #9 from biopython-bugzilla at maubp.freeserve.co.uk  2009-12-21 10:34 EST -------
(In reply to comment #8)
> (In reply to comment #7)
> Just to confirm that I can reproduce the 'Query: 0' with blastpgp 2.2.22
> using Robson's test case. Thanks to Robson for this and apologies for not
> having been able to send a test case.

I was also able to confirmed the problem is present in blastpgp 2.2.22,
however it seems to have been fixed in the "new" BLAST+ suite, psiblast
2.2.22+ as described here:
http://lists.open-bio.org/pipermail/bioperl-l/2009-December/031811.html

Given this new information, this does look like an NCBI BLAST bug, and not
a problem in Biopython itself. We *might* be able to get our parser to cope
with the funny BLAST output, but it does look difficult and risky to me.

Miguel - Is it possible the BLAST bug is relatively recent and first showed
up when you updated blastpgp to 2.2.18?

Regards,

Peter


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