[Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Dec 8 05:45:12 EST 2004


------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2004-12-08 05:45 -------
Created an attachment (id=184)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=184&action=view)
RPS-BLAST 2.2.9 output file for testing rpsblast support

I am pleased to report that with my proposed changes, the
Bio/Tests/test_NCBIStandalone.py program still runs without error.

The attachment (bt071) is an additional test file (currently the next free slot
is bt071) to go here Bio/Tests/Blast/bt071

It is the output of RPS-BLAST 2.2.9 [May-01-2004] when fed a KdpE (225 letters)
from E.coli against the Pfam database from the NCBI.

Adding bt071 to Bio/Tests/test_NCBIStandalone.py works as expected.

Note - With rpsblast 2.2.9 and 2.2.10, the output file DOES NOT appear to
include any reference to the database used.

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