[Bioperl-l] parsing a BLAST output

[Angshu Kar]

Thanks Brian.


On 12/5/05, Brian Osborne <osborne1 at optonline.net> wrote:
>
> Angshu,
>
> It looks like there's WU Blast output used in various tests:
>
> t/data/dnaEbsub_ecoli.wublastx
> t/data/ecolitst.wublastp
> t/data/ecolitst.noseqs.wublastp
>
>
> Brian O.
>
>
> On 12/4/05 8:32 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:
>
> > Hi,
> >
> > To begin with, I'm new to Bioperl.
> > Now, I've written the following simple piece of code to parse a WU-Blast
> > output which filters data *for a given e-value and >50% overlap*.
> >
> > I'm writing the main algorithm here:
> >
> > my $blast_report = $ARG[1];
> > my $threshold_evalue = $ARG[2];
> >
> > my $in = new Bio::SearchIO(-format => 'blast', -file => $blast_report);
> >
> > while (my $result = $in -> next_result)
> >    {
> >       while(my $hit = $result->next_hit)
> >          {
> >             if(($line{$hit->name} == $line{$result->query_accession}))
> >                {
> >                   next;
> >                }
> >             if($hit->hsp->evalue <= $threshold_evalue)
> >                {
> >                   if($hit->hsp->frac_indentical>=0.5)
> >                      {
> >                         print $line{$result->query_accession} . "\t" .
> > $line{$hit->name} . "\t" . $hit->hsp-evalue . "\n";
> >                     }
> >               }
> >       }
> > }
> >
> > My questions are:
> >
> > 1. does the frac_identical gives the measure of % overlap? Or, are there
> any
> > other methods?
> > 2. now, i don't have any blast data sets to test my code upon.could any
> of
> > the experienced users let me know whether the algorithm is fine?any
> > tip-offs on any point (from optimization to syntactical errors) are
> heartily
> > welcome.
> > 3. could any one please let me know if i can find sample wu-blast
> outputs to
> > test my script upon?
> >
> > Appreciate your guidance.
> >
> > Thanks,
> > Angshu
> >
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> > Bioperl-l at portal.open-bio.org
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>
>
>