/usr/share/perl5/Bio/Tools/Tmhmm.pm is in libbio-perl-perl 1.6.923-1.
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# BioPerl module for Bio::Tools::Tmhmm
#
# Original copyright Balamurugan Kumarasamy
# Re-written cleanly by Torsten Seemann, Sep 2006
#
# Copyright:
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
=head1 SYNOPSIS
use Bio::Tools::Tmhmm;
my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle );
while ( my $tmhmm_feat = $parser->next_result ) {
# do something, e.g.
push @tmhmm_feat, $tmhmm_feat;
}
=head1 DESCRIPTION
TMHMM is software for the prediction of transmembrane helices in proteins.
See L<http://www.cbs.dtu.dk/services/TMHMM/> for more details.
This module parses the "long output" format of TMHMM 2.0 and
creates a Bio:SeqFeature::Generic object for each C<TMHelix> feature found
from lines like this:
my_sequence_id TMHMM2.0 TMhelix 54 76
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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/
=head1 AUTHOR - Torsten Seemann
Email torsten.seemann AT infotech.monash.edu.au
=head1 CONTRIBUTOR - Bala
Email savikalpa@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Tools::Tmhmm;
use strict;
use Bio::Tools::AnalysisResult;
use Bio::Root::Root;
use Bio::Root::IO;
use base qw(Bio::Root::Root Bio::Root::IO Bio::Tools::AnalysisResult);
use Bio::SeqFeature::Generic;
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Tmhmm->new();
Function: Builds a new Bio::Tools::Tmhmm object
Returns : Bio::Tools::Tmhmm
Args : Either of the following as per L<Bio::Root::IO> interface
-fh => $filehandle
-file => $filename
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : my $feat = $Tmhmm->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
=cut
sub next_result {
my $self = shift;
# # my_sequence_id Length: 178
# my_sequence_id TMHMM2.0 outside 1 53
# my_sequence_id TMHMM2.0 TMhelix 54 76
# my_sequence_id TMHMM2.0 inside 77 115
while (my $line = $self->_readline) {
if ( $line =~ m/^(\S+)\s+(\S+)\s+(TMhelix)\s+(\d+)\s+(\d+)$/i ) {
return Bio::SeqFeature::Generic->new(
-primary => 'transmembrane',
-seq_id => $1,
-source => $2,
-start => $4,
-end => $5,
);
}
}
}
1;
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