[Bioperl-l] Fwd: blast.pm patch

Robson Francisco de Souza robfsouza at gmail.com
Sat Dec 19 06:06:16 EST 2009

Hi Peter,

I just upload my example. I also reported this bug to the NCBI
developers and I hope they can fix it, since it is easy to reproduce.
I just forgot to mention the blastpgp version: 2.2.18

On Fri, Dec 18, 2009 at 6:00 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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?:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2927
> Thanks!
> Peter @ Biopython

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