Bio::SearchIO hmmer
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Summary
Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
Package variables
No package variables defined.
Included modules
Bio::Factory::ObjectFactory
Inherit
Bio::SearchIO
Synopsis
    # 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";
}
}
}
Description
This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3
Methods
new
No description
Code
_initialize
No description
Code
Methods description
None available.
Methods code
newdescriptionprevnextTop
sub new {
  my ( $caller, @args ) = @_;
  my $class = ref($caller) || $caller;

  my $self = $class->SUPER::new(@args);
  $self->_initialize(@args);

  # Try to guess the hmmer format version if it's not specified.
my $version; 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 { # read second line of the file
my $first_line = $self->_readline; $_ = $self->_readline; if ( m/HMMER\s3/ ) {
$version = "3";
} else { $version = "2"; } $self->_pushback($_); $self->_pushback($first_line); } my $format = "hmmer$version"; return unless( $class->_load_format_module($format) ); bless($self, "Bio::SearchIO::$format"); return $self;
}
_initializedescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Kai BlinTop
Email kai.blin-at-biotech.uni-tuebingen.de
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _