[BioPython] NCBIXML - Blast in- and output

[Björn Thorwirth]

Hi Michiel!

Thanks for your fast respose! I've used the NCBIXML together with a
Twisted server. That's why the backtrace is a bit bloatet.
But I guess this are the important lines:

File "/home/user/workspace/PLGDaemon/src/mmCIF/blast_util.py", line
56,
in getResults
    for record in records:
  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.

Now i was able to backtrace, where the Problem comes from. It may not be
related to 32/64 Bit. It happens when Blast's calculation 
of the "Karlin-Altschul parameters" fails. This may happen due low
complexity of the Query sequence (see Blast FAQ).
I've attached a tar with the Blast-output and the reference and input
files. I didn't stumble over this problem before on 32 Bit,
because that was a smaller Sequenze-DB for testing purposes

Björn

Am Dienstag, den 27.11.2007, 21:25 +0900 schrieb Michiel de Hoon:
> Can you create a minimal code example that shows this bug?
>  From the Python traceback, it appears that the error does not occur
in 
> NCBIXML but some place else. It would be good to isolate this bug to 
> find out where exactly the problem lies.
> 
> --Michiel.
> 
> Björn Thorwirth wrote:
> > Hello List!
> > 
> > Today i got some trouble with the NCBIXML module. I've tested my
code on
> > a
> > 32-Bit machine with Biopython-1.43 where it worked flawless.  On
64-Bit
> > i
> > got the this error with Biopython-1.43 / 1.44:
> > 
> > 
> 
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