[Bioperl-l] parsing a BLAST output

[Brian Osborne]

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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l