[Biopython-dev] [Bug 2412] New: NCBIXML. fails parsing with blast 2.2.15 in special cases (Karlin-Altschul)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2412

           Summary: NCBIXML. fails parsing with blast 2.2.15 in special
                    cases (Karlin-Altschul)
           Product: Biopython
           Version: 1.44
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bjoern.thorwirth at uni-due.de


this is the blas call i used:  blastall -pblastp -dreference.fasta
-i/home/user/workspace/PLGDaemon/src/working_directories/blast_plugin/input2.fasta
-MPAM250 -m7 -e0.01 -gt -G-1 -E-1
XML output is empty.
Here is the Backtrace i got:
<omitted> (Twisted Stuff)
  File
"/home/user/Desktop/biopython/biopython-1.43/build/lib.linux-x86_64-2.4/Bio/Blast/NCBIXML.py",
line 625, in parse
    assert len(blast_parser._records) == 0
exceptions.UnboundLocalError: local variable 'blast_parser' referenced before
assignment
<omitted> (Twisted stuff)


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