[Biopython-dev] [Bug 1929] New: Extra reference in BLASTPGP plain text output

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1929

           Summary: Extra reference in BLASTPGP plain text output
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


Reported on the mailing list by Alessandro Nascimento, 

http://portal.open-bio.org/pipermail/biopython/2006-January/002883.html

BLASTP 2.2.12 [Aug-07-2005] and possibly other versions include a second
reference which breaks the plain text blast parser:

Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravaind, 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.
29:2994-3005.

Removing these lines from the blast output allows the file to be parsed.

I tested this on BioPython 1.41, Python 2.4 under linux




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