[Bioperl-l] Putative bug in Bio/SearchIO/blast.pm
jason.stajich at duke.edu
Sun Jun 12 16:15:36 EDT 2005
I'm pretty sure this is already fixed with the code in CVS. Can you
try it with that code -- the regexp was already corrected in
connection to very large bitscores (Scott Markel's bug) - it is done
slightly differently from your suggested fix as we need to handle sci-
value in that field as well.
Also, please post bugs and diffs to http://bugzilla.open-bio.org so
that they can be tracked - otherwise folks have to follow a mailing
list thread to find out the resolution for a bug.
On Jun 9, 2005, at 8:58 AM, Jérémy JUST wrote:
> I think I've found a little bug in the Blast parser.
> On that Blast result (BLASTN 2.2.9 [May-01-2004]):
> Score E
> Sequences producing significant alignments:
> (bits) Value
> gi|42592260|ref|NC_003070.5| Arabidopsis thaliana chromosome
> 1, ... 75.8 8e-13
>> gi|42592260|ref|NC_003070.5| Arabidopsis thaliana chromosome 1,
> Length = 30432563
> Score = 75.8 bits (38), Expect = 8e-13
> Identities = 104/126 (82%)
> Strand = Plus / Minus
> the score is read as « 8 » instead of « 75.8 ».
> I attach a tiny patch against Bioperl-1.5.0.
> ($Id: blast.pm,v 1.84 2004/10/28 20:40:12 jason Exp $)
> Jérémy JUST <jeremy_just at netcourrier.com>
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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