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";
            }
        }
    }

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#
# BioPerl module for Bio::SearchIO::hmmer
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Kai Blin <kai.blin@biotech.uni-tuebingen.de>
#
# Copyright Kai Blin
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

# Let the code begin...

package Bio::SearchIO::hmmer;

use strict;

use Bio::Factory::ObjectFactory;

use base qw(Bio::SearchIO);

sub new {
  my ( $caller, @args ) = @_;
  my $class = ref($caller) || $caller;

  if( $class =~ /Bio::SearchIO::hmmer(\d)/ ) {
    my ($self) = $class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;
  } else {
    # Try to guess the hmmer format version if it's not specified.
    my $version;
    my $fh;
    my $fh_needs_close = 0;
    my %param = @args;

    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys

    # If the caller specified a version, go for that
    if (defined($param{"-version"})) {
      $version = $param{"-version"};
    } else {
      # Check the contents of the file for the hmmer version mentioned in there
      if (defined($param{"-fh"})) {
          $fh = $param{"-fh"};
      } elsif (defined($param{"-file"})) {
        open($fh, $param{"-file"}) || return;
        $fh_needs_close = 1;
      }

      # read second line of the file
      <$fh>;
      $_ = <$fh>;

      if ( m/HMMER\s3/ ) {
        $version = "3";
      } else {
        $version = "2";
      }

      if ($fh_needs_close) {
          close($fh);
      } else {
          seek($fh, 0, 0);
      }
    }

    my $format = "hmmer$version";
    return unless( $class->_load_format_module($format) );
    return "Bio::SearchIO::${format}"->new(@args);
  }
}

sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my $handler = $self->_eventHandler;
    $handler->register_factory(
        'result',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Result::HMMERResult',
            -interface => 'Bio::Search::Result::ResultI'
        )
    );

    $handler->register_factory(
        'hit',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Hit::HMMERHit',
            -interface => 'Bio::Search::Hit::HitI'
        )
    );

    $handler->register_factory(
        'hsp',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::HSP::HMMERHSP',
            -interface => 'Bio::Search::HSP::HSPI'
        )
    );
}

1;