[Bioperl-l] NEED HELP URGENTLY

Simon Andrews simon.andrews at bbsrc.ac.uk
Fri Sep 1 11:37:42 EDT 2006


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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