Bioperl: Blast.pm as BLAST filter?

[Ian Korf]

Christian,

I've mangled a bit of my code to give you something which might be useful
to you. It allows you to read any BLAST report and filter it for scores,
percent identities, and P (or E) values for the HSPs and filter the Sbjcts
by their name. So you can get only those alignments better than score 100,
percent 90, and P 1e-20, and further get rid of anything matching "sapiens"
for example. The usage statement is pretty clear. It spits out the original
BLAST output. I haven't altered the header, so even if you filter off all
your alignments, you'll still have the summary info. It reads a file and
outputs to STDOUT. You may want to make the trivial change of it reading
from STDIN so you can pipe away.

-Ian Korf


> From owner-vsns-bcd-perl@lists.uni-bielefeld.de  Fri Dec 10 03:43:35 1999
> Delivered-To: ikorf@sapiens.wustl.edu
> From: Christian Gruber <gruber@mips.biochem.mpg.de>
> Mime-Version: 1.0
> Content-Transfer-Encoding: 7bit
> Date: Fri, 10 Dec 1999 10:37:14 +0100 (MET)
> To: vsns-bcd-perl@lists.uni-bielefeld.de
> Subject: Bioperl: Blast.pm as BLAST filter?
> X-URL: http://bio.perl.org/
> X-Administrativa: see footer; if necessary, email to vsns-bcd-perl-owner@lists.uni-bielefeld.de
> 
> Hello!
> 
> I have a problem concerning BioPerl::Tools::Blast.
> 
> I'd like to take a huge BLAST result file, parse it using this class,
> filter the hits that are interesting, and then print it in the
> 'natural' BLAST output format.
> 
> The first three steps work fine (and really easily!!), but what does
> not work as easily is the printing of the Blast object. There is a
> method "to_html" that does kind-of what I mean, but I'd like it in raw
> text format, like BLAST has produced. Just with a few hits missing.
> 
> So: Is there an easy way to print a Bio::Tools::Blast object?
> 
> 
> Thanks in advance
> 
> Christian Gruber
> 
> 
> --
> Christian Gruber      gruber@mips.biochem.mpg.de
>                       Tel: +49 - 89 / 8578-2663
> MIPS - Munich Information Center for Protein Sequences
> http://www.mips.biochem.mpg.de
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