[Bioperl-l] NEED HELP URGENTLY

Chris Fields cjfields at uiuc.edu
Fri Sep 1 12:11:20 EDT 2006


I plan on looking at this one this weekend.  I would suggest trying  
XML output parsing to see if that helps.

Chris


On Sep 1, 2006, at 10:37 AM, Simon Andrews wrote:

>
> On 1 Sep 2006, at 11:57, neeti somaiya wrote:
>
>> Hi,
>>
>> I have written a BLAST parser script, and when I try running it on
>> a BLASTN
>> ouput file to get the first 10 hits, it gives me 10 random hits,
>> and not the
>> first 10 hits.Can anyone give me any idea what could be the cause
>> of this
>> behaviour of the parser.
>
> Looking at your blast file you appear to have duplicate entries in
> your blast database (more than one hit to the same accession).  In
> that case your problem is probably this:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=1986
>
> There are patches and workrounds listed in the bug report, but
> there's no real fix as yet.
>
> Hope this helps
>
> Simon.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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