[Biopython-dev] [Bug 1735] New: Bio.Blast.NCBIStandalone.BlastParser crashs with unusual alignment fragments

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1735

           Summary: Bio.Blast.NCBIStandalone.BlastParser crashs with unusual
                    alignment fragments
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: gebauer-jung at ice.mpg.de


This is possibly rather a problem of the blastall program
than a bug of the parser, but maybe the parser should 
be able to handle it.

I will attach the blast output which crashes the parser 
due to the crazy fragment within the last alignment.

Following parameters were used for blastall:
-p blastn
-F F (filter off)
-g (gapped blast)
-G 1 (gap opening penalty)
-E 1 (gap extension penalty)

The parser crashes with the message:
    SyntaxError: I could not find the query in line
    Query: 0   --

Thanks



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