[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
Fri May 23 14:30:42 UTC 2008


------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-23 10:30 EST -------
I'm using the CVS version of Biopython under Linux.  The file main
NCBIStandalone.py hasn't changed since Biopython 1.45, although Record.py has.

I am a little puzzled about why I can parse both the 2.2.15 and the 2.2.18
plain text examples you provided without problems, but something fails for you.
 Could you double check what happens on your machine using these two example
files from attachment 922 comment 3, and this code I gave in comment 4:

from Bio.Blast import NCBIStandalone
for filename in ["blastpgp.2.2.15.txt", "blastpgp.2.2.18.txt"] :
    print filename
    print "="*len(filename)
    handle = open(filename)
    record = NCBIStandalone.PSIBlastParser().parse(handle)
    print record.query
    if record.converged : print '*** Converged!!! ***'
    for iter_round in record.rounds :
        print "Iteration with %i alignments" \
              % (len(iter_round.alignments))
        print "%i new sequences, %i reused" \
              %(len(iter_round.new_seqs), len(iter_round.reused_seqs))
    print "End of plain text output"

If this doesn't work, please give the full stack trace - "chokes" is a little

Looking at the example files you provided in attachment 922 comment 3, they
seem to have replaced one reference with another.  This is the start of the
diff output comparing the two files:

< BLASTP 2.2.15 [Oct-15-2006]
> BLASTP 2.2.18 [Mar-02-2008]
< Reference for composition-based statistics:
< Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
< Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
< Eugene V. Koonin, and Stephen F. Altschul (2001), 
< "Improving the accuracy of PSI-BLAST protein database searches with 
< composition-based statistics and other refinements",  Nucleic Acids Res.
> Reference for compositional score matrix adjustment: Altschul, Stephen F., 
> John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
> Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
> using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

This reference change doesn't seem to cause a problem on my machine.  I didn't
notice anything else worth commenting about.

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