[Bioperl-l] parsing a BLAST output

Angshu Kar angshu96 at gmail.com
Sun Dec 4 20:32:20 EST 2005


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}))
            if($hit->hsp->evalue <= $threshold_evalue)
                        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
3. could any one please let me know if i can find sample wu-blast outputs to
test my script upon?

Appreciate your guidance.


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