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

[Ian Korf]

The latest version of BPlite also reads concatenated blast reports. So you
can do the following:

my $multi = new BPlite::Multi(\*FILEHANDLE);
while (my $blast = $multi->nextBlast) {
    while (my $sbjct = $blast->nextSbjct) {
        print "$sbjct\n";
    }
}

Unfortunately, BPlite has two development branches, the bioperl one and my
own (sorry about that). But the new code should be trivial to migrate.

-Ian

On Wed, 11 Oct 2000, Jason Stajich wrote:

> 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
> file.
> 
> > 
> > 	Hilmar
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                                email: hlapp@gmx.net
> > NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> > A-1235 Vienna                                fax: +43 1 86634 727
> > -----------------------------------------------------------------
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> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office) 
> (919)684-2275 (fax) 
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/ 
> 
> 
> 
> 
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