[Bioperl-l] parsing a BLAST output

[Angshu Kar]

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