Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)

SYNOPSIS

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  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;
  }

DESCRIPTION

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TMHMM is software for the prediction of transmembrane helices in proteins. See 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 TMHelix feature found from lines like this:

  my_sequence_id  TMHMM2.0  TMhelix     54    76

FEEDBACK

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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

Support

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 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/

AUTHOR - Torsten Seemann

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Email torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - Bala

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Email savikalpa@fugu-sg.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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


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;



sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  return $self;
}



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;