[Bioperl-l] Fwd: blast.pm patch

Peter biopython at maubp.freeserve.co.uk
Fri Dec 18 18:00:47 EST 2009

On Fri, Dec 18, 2009 at 6:07 PM, Robson Francisco de Souza
<robfsouza at gmail.com> wrote:
> Hi,
> I've been dealing with an apparent bug in the output of NCBI's BLAST
> programs (blastall, blastpgp) which sometimes produces output like the
> one below.
> I think I've managed to produce a work around for Bioperl blast.pm
> parser and would like to contribute it to Bioperl.
> The fix is based on blast.pm from the CVS tree (downloaded some months
> ago...) and is attached to this message.
> Best,
> Robson

Do you have a complete example of this kind of funny output?
This problem has also been reported with blastpgp for the
Biopython parser. I'd love an example for our unit tests
(probably worth doing in BioPerl too). Could you upload a
test case here?:



Peter @ Biopython

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