[Bioperl-l] parsing only the summary part of a blast report

Jason Stajich jason@chg.mc.duke.edu
Wed, 11 Oct 2000 09:18:40 -0400 (EDT)

see the perldoc for Bio::Tools::BPlite for all the complete api.

This script will parse and print all of the hits in your report.

#!/usr/local/bin/perl -w

use Bio::Tools::BPlite;

my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
print $report->query(), ",", $report->database(), "\n";
while ( my $sbjct = $report->nextSbjct ) {
    print "name is ", $sbjct->name(), "\n";

Alternatively you can use Bio::Tools::Blast, but you will find it slower
and more memory intensive.  It does support more features so it depends on
what your needs are.

On Wed, 11 Oct 2000, Hilmar Lapp wrote:

> > "Zhao, David [PRI]" wrote:
> > 
> > Hi there,
> > How can I parse the summary part of a blast report using bioperl
> > modules? such as:
> > 
> I'm almost sure you can't using Blast.pm. Maybe you can with BPlite
> (development trunk only). I know that Blast.pm takes a signifant time to
> parse long reports (i.e., with  hundreds of alignments), but we haven't
> checked yet whether BPlite is significantly faster in such cases. I guess
> you're asking because you bother about the time lost in parsing the
> alignments, although you needed only the summary data which are already
> present in the hit list.
> BTW you can pass a significance threshold to Blast.pm, and although I'm
> not sure I think it won't parse those alignments beyond the significance
> threshold.

[Regarding Bio::Tools::Blast]

I'm pretty sure the signifigance threshold only applies to when you are
running Blast not parsing a report.  In fact you should not put a
signif=>$value in your parameter hash if you are just parsing a report

> 	Hilmar
> -- 
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> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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Jason Stajich
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center