[Bioperl-l] GenericResult.pm and HMMERResult.pm question

Diane Benz (CCGB) diane at mail.ahc.umn.edu
Fri Mar 14 11:16:04 EST 2003


Hello,
I am trying to parse and extract some information from a hmmpfam report
using bioperl. I have a list of fields that I would like to extract, but
I am having problems extracting fields such as the accession number
through methods $result->query_accession(),  $result->query_length() and
others. Should I be able to extract these fields? This is in essence how
I am using bioperl:

use Bio::SearchIO;

.
.
.
my $report = new Bio::SearchIO(-format => 'hmmer',
                                                        -fh         =>
\*filehandle);

while (my $result = $report->next_result) {
  while (my $hit = $result->next_hit) {
      while (my $hsp = $hit->next_hsp) {
           print $result->query_accession();
           print $result->query_length();
       }
  }
}


I would appreciate any suggestions.
Thanks, Diane Benz











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