Bio::Tools Tmhmm
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Summary
Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SeqFeature::Generic
Bio::Tools::AnalysisResult
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
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $feat = $Tmhmm->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  return $self;
}
next_resultdescriptionprevnextTop
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;
}
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
Support Top
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 - Torsten SeemannTop
Email torsten.seemann AT infotech.monash.edu.au
CONTRIBUTOR - BalaTop
Email savikalpa@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _