Bio::SearchIO::hmmer(3pm) | User Contributed Perl Documentation | Bio::SearchIO::hmmer(3pm) |
Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
# do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), "\n"; while( my $hit = $result->next_hit ) { print $hit->name(), "\n"; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), "\n"; } } }
This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
2019-10-29 | perl v5.30.0 |