[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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