[Biopython-dev] [Bug 2502] PSIBlastParser fails with blastpgp 2.2.18 though works with blastpgp 2.2.15

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Jun 2 08:49:55 UTC 2008


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

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

------- Comment #20 from biopython-bugzilla at maubp.freeserve.co.uk  2008-06-02 04:49 EST -------
Marking this bug as fixed.

The original report was about parsing the plain text output which is fixed -
see comment 12, and Bio/Blast/NCBIStandalone.py CVS revision 1.72.  I have not
added the 2.2.18 plain text file as a unit test since its over 750kb.

For the XML output from 2.2.18, as far as I can tell we are not ignoring any
important information from PSI-BLAST, as it is simply not included.  If the
NCBI updates the XML output from blastpgp then we should revisit the XML

Thank you Miguel for your report and assistance.

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