[Bioperl-l] problems with blast parser

Chris Fields cjfields at uiuc.edu
Thu Apr 6 11:56:58 EDT 2006


Alessandro,

We need to know a few things first:

1)  What version of Bioperl? 
2)  BLAST version?
3)  What OS?
4)  Perl version?
5)  Exactly how large is your file?

It would also be nice to see at least a chunk of your script to rule out a
logic error there.  If you want you can also submit your script by filing
this as a bug in Bugzilla and attaching your script.  

http://www.bioperl.org/wiki/Bugs

If you have an older version of Bioperl (such as 1.4) consider upgrading to
1.5.1 or CVS.  Lots of fixes have been incorporated since 1.4, including to
SearchIO.

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Alessandro S. Nascimento
> Sent: Tuesday, April 04, 2006 10:28 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] problems with blast parser
> 
> Hi all
> 
> I'm trying to parse a blast standalone (blaspgp) result file and filter
> some sequences using length and identity. The script used to work but
> this time after several minutes working in 99.9% of my processor I have
> a "killed"message with no more information. The blast file is very
> large. Does anyone have any clue ?
> 
> Thanks in advance
> 
> Alessandro
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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