[Bioperl-l] HMMER - Parse hmmpfam output using bioperl - help!!

K. Shameer shameer at ncbs.res.in
Thu May 8 07:11:45 EDT 2008


Dear All,

Here is the code snippet I used to get the hit name and hit length from an
hmmpfam file. I need to add the sequence start and end information
(query), description of domain, score and e-value.

I checked for the available method in deobfuscator, but I couldn't find
the details i wanted. Is there methods available in the Bio::SearchIO or
related modules.
__CODE__
$input = shift;
use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer',
                               -file   => $input);
    while( my $result = $in->next_result ) {
        while( my $hit = $result->next_hit ) {
            print $hit->name(),"\t";
            while( my $hsp = $hit->next_hsp ) {
                print $hsp->length(), "\n";
            }
        }
    }
_END_

Result for test.pf
TRAP_240kDa     680

--
Thanks in advance,
K. Shameer



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