lib/Bio/Tools/Tmhmm.pm

   1 #
   2 # BioPerl module for Bio::Tools::Tmhmm
   3 #
   4 # Original copyright Balamurugan Kumarasamy
   5 # Re-written cleanly by Torsten Seemann, Sep 2006
   6 #
   7 # Copyright:
   8 # You may distribute this module under the same terms as Perl itself
   9
  10 =head1 NAME
  11
  12 Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
  13
  14 =head1 SYNOPSIS
  15
  16   use Bio::Tools::Tmhmm;
  17   my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle );
  18   while ( my $tmhmm_feat = $parser->next_result ) {
  19      # do something, e.g.
  20      push @tmhmm_feat, $tmhmm_feat;
  21   }
  22
  23 =head1 DESCRIPTION
  24
  25 TMHMM is software for the prediction of transmembrane helices in proteins.
  26 See  L<http://www.cbs.dtu.dk/services/TMHMM/> for more details.
  27
  28 This module parses the "long output" format of TMHMM 2.0 and
  29 creates a Bio:SeqFeature::Generic object for each C<TMHelix> feature found
  30 from lines like this:
  31
  32   my_sequence_id  TMHMM2.0  TMhelix     54    76
  33
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via the
  61 web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Torsten Seemann
  66
  67 Email torsten.seemann AT infotech.monash.edu.au
  68
  69 =head1 CONTRIBUTOR - Bala
  70
  71 Email savikalpa@fugu-sg.org
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80 package Bio::Tools::Tmhmm;
  81
  82 use strict;
  83
  84 use Bio::Tools::AnalysisResult;
  85 use Bio::Root::Root;
  86 use Bio::Root::IO;
  87
  88 use base qw(Bio::Root::Root Bio::Root::IO Bio::Tools::AnalysisResult);
  89
  90 use Bio::SeqFeature::Generic;
  91
  92
  93 =head2 new
  94
  95  Title   : new
  96  Usage   : my $obj = Bio::Tools::Tmhmm->new();
  97  Function: Builds a new Bio::Tools::Tmhmm object
  98  Returns : Bio::Tools::Tmhmm
  99  Args    : Either of the following as per L<Bio::Root::IO> interface
 100              -fh   => $filehandle
 101              -file => $filename
 102
 103 =cut
 104
 105 sub new {
 106   my($class,@args) = @_;
 107   my $self = $class->SUPER::new(@args);
 108   $self->_initialize_io(@args);
 109   return $self;
 110 }
 111
 112
 113 =head2 next_result
 114
 115  Title   : next_result
 116  Usage   : my $feat = $Tmhmm->next_result
 117  Function: Get the next result set from parser data
 118  Returns : Bio::SeqFeature::Generic
 119  Args    : none
 120
 121 =cut
 122
 123 sub next_result {
 124   my $self = shift;
 125
 126   # # my_sequence_id Length: 178
 127   # my_sequence_id  TMHMM2.0  outside      1    53
 128   # my_sequence_id  TMHMM2.0  TMhelix     54    76
 129   # my_sequence_id  TMHMM2.0  inside      77   115
 130
 131   while (my $line = $self->_readline) {
 132     if ( $line =~ m/^(\S+)\s+(\S+)\s+(TMhelix)\s+(\d+)\s+(\d+)$/i ) {
 133        return Bio::SeqFeature::Generic->new(
 134          -primary => 'transmembrane',
 135          -seq_id  => $1,
 136          -source  => $2,
 137          -start   => $4,
 138          -end     => $5,
 139        );
 140     }
 141   }
 142 }
 143
 144 1;
 145
 146