[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]

http://bugzilla.open-bio.org/show_bug.cgi?id=2502





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-21 09:05 EST -------
Miguel - could you also attach the XML output from blastpgp 2.2.15 and 2.2.18
please?

e.g.  Something like this if you want to do it via Biopython:

blast_out, error_info = NCBIStandalone.blastpgp(
        blastcmd='/opt/Bio/blast-2.2.15/bin/blastpgp',
        database='/opt/databases/BlastDB/nrdb100ncbi',
        infile=file,
        npasses=passes,
        align_view='0',
        matrix_outfile=file + '.pssm')

handle = open("blastpgp_2.2.15.xml","w")
handle.write(blast_out.read())
handle.close()

Thanks, Peter.


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