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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1715


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

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




------- Comment #12 from biopython-bugzilla at maubp.freeserve.co.uk  2006-03-09 11:24 -------
Marking as fixed - as long as you use XML output, not plain text.

See also Bug 1933 which fixes standalone blast XML iteration, and has some
examples attached using rpsblast output.

I have checked in a new "rpsblast" function to Bio/Blast/NCBIStandalone.py
based on the existing "blastall" and "blastpgp" functions.

However, this will by default call standalone RPS-BLAST with the option -m 7 to
produce XML output.

See Bio/Blast/NCBIStandalone.py revision 1.60

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython

NOTE - BioPython does not currently support the "plain text" default output
from standalone rpsblast, especially for multiple queries.




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