Summary

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

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root Bio::Tools::AnalysisResult

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;
  }

Description

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

Methods

Methods description

 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 Bio::Root::IO interface
             -fh   => $filehandle 
             -file => $filename

 Title   : next_result
 Usage   : my $feat = $Tmhmm->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none

Methods code

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,
       );
    }
  }

}

General documentation

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

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:

  http://bugzilla.open-bio.org/

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

Email savikalpa@fugu-sg.org

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