[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
Wed Oct 14 12:41:23 UTC 2009


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
             Status|NEW                         |RESOLVED
         Resolution|                            |WORKSFORME

------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2009-10-14 08:41 EST -------
As discussed on the mailing list, something about how blastpgp was being
called via subprocess could lead to strange unparseable output. There may
be some subtle issue with Bio.Blast.NCBIStandalone.blastpgp here, but in
the long term that function will be phased out anyway. Miguel is now
using Bio.Blast.Applications and subprocess to get BLAST to record its
output directly to a file, and the problem has gone away.

I'm closing this bug by marking it as "WORKSFORME" rather than "FIXED".

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