Bio/Tools/Match.pm

   1 # $Id: Match.pm,v 1.2 2007/06/14 18:01:52 nathan Exp $
   2 #
   3 # BioPerl module for Bio::Tools::Match
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Sendu Bala
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Tools::Match - Parses output from Transfac's match(TM)
  18
  19 =head1 SYNOPSIS
  20
  21   use strict;
  22
  23   use Bio::Tools::Match;
  24
  25   my $parser = Bio::Tools::Match->new(-file => "match.out");
  26
  27   while (my $feat = $parser->next_result) {
  28     my $start = $feat->start;
  29     my $end = $feat->end;
  30     my $core_score = $feat->score;
  31     my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
  32     my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
  33   }
  34
  35 =head1 DESCRIPTION
  36
  37 This module is used to parse the output from Transfac's match(TM) program. It
  38 doesn't support the histogram output of match.
  39
  40 Each result is a Bio::SeqFeature::Annotated representing a single matrix match.
  41
  42 =head1 FEEDBACK
  43
  44 =head2 Mailing Lists
  45
  46 User feedback is an integral part of the evolution of this and other
  47 Bioperl modules. Send your comments and suggestions preferably to
  48 the Bioperl mailing list. Your participation is much appreciated.
  49
  50   bioperl-l@bioperl.org                  - General discussion
  51   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  52
  53 =head2 Support
  54
  55 Please direct usage questions or support issues to the mailing list:
  56
  57 I<bioperl-l@bioperl.org>
  58
  59 rather than to the module maintainer directly. Many experienced and
  60 reponsive experts will be able look at the problem and quickly
  61 address it. Please include a thorough description of the problem
  62 with code and data examples if at all possible.
  63
  64 =head2 Reporting Bugs
  65
  66 Report bugs to the Bioperl bug tracking system to help us keep track
  67 of the bugs and their resolution. Bug reports can be submitted via the
  68 web:
  69
  70   https://github.com/bioperl/bioperl-live/issues
  71
  72 =head1 AUTHOR - Sendu Bala
  73
  74 Email bix@sendu.me.uk
  75
  76 =head1 APPENDIX
  77
  78 The rest of the documentation details each of the object methods.
  79 Internal methods are usually preceded with a _
  80
  81 =cut
  82
  83 # Let the code begin...
  84
  85 package Bio::Tools::Match;
  86 use strict;
  87
  88 use Bio::SeqFeature::Generic;
  89 use Bio::Annotation::SimpleValue;
  90
  91 use base qw(Bio::Root::Root Bio::Root::IO);
  92
  93
  94 =head2 new
  95
  96  Title   : new
  97  Usage   : my $obj = Bio::Tools::Match->new();
  98  Function: Builds a new Bio::Tools::Match object
  99  Returns : Bio::Tools::Match
 100  Args    : -file (or -fh) should contain the contents of a standard match output
 101
 102 =cut
 103
 104 sub new {
 105     my ($class, @args) = @_;
 106     my $self = $class->SUPER::new(@args);
 107
 108     $self->_initialize_io(@args);
 109
 110     return $self;
 111 }
 112
 113 =head2 next_result
 114
 115  Title   : next_result
 116  Usage   : $result = $obj->next_result();
 117  Function: Returns the next result available from the input, or undef if there
 118            are no more results.
 119  Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
 120            for 'matrix_score', 'matrix_id' and a 'predicted' tag.
 121  Args    : none
 122
 123 =cut
 124
 125 sub next_result {
 126     my ($self) = @_;
 127
 128     my $line = $self->_readline || return;
 129
 130     if (! $self->{found_seq_id} && $line =~ /^Inspecting sequence ID\s+(.+)/) {
 131         $self->{found_seq_id} = $1;
 132     }
 133
 134     while ($line !~ /^\s\S+\s+\|\s+\d+/) {
 135         $line = $self->_readline || return;
 136     }
 137
 138
 139     # The first column gives the TRANSFAC(r) identifier of the matching matrix,
 140     # then comes the position and the strand where the respective match has been
 141     # found. The core similarity score is given in column three, the matrix
 142     # similarity score in column four. The last column gives the matching
 143     # sequence.
 144     #
 145     #
 146     #Search for sites by WeightMatrix library: /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat
 147     #Sequence file: sequence.fa
 148     #Site selection profile: mxprf Profile generated from /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat with default values.
 149     #
 150     #
 151     #Inspecting sequence ID   Homo_sapiens
 152     #
 153     # V$MYOD_01              |        5 (+) |  0.751 |  0.784 | ttaGAGGTggcg
 154     # V$MYOD_01              |        5 (-) |  0.778 |  0.580 | ttagAGGTGgcg
 155     # V$MYOD_01              |       30 (+) |  0.751 |  0.581 | gctCAGGCaccc
 156     #[...]
 157     # V$RORA_Q4              |    53610 (+) |  0.775 |  0.668 | tgtgggGGCCA
 158     # V$RORA_Q4              |    53639 (+) |  0.775 |  0.636 | gtcgggGGACA
 159     #
 160     # Total sequences length=53654
 161     #
 162     # Total number of found sites=1735559
 163     #
 164     # Frequency of sites per nucleotide=32.347243
 165
 166     my ($matrix_id, $start, $strand, $core_score, $matrix_score, $seq) = $line =~ /^\s(\S+)\s+\|\s+(\d+)\s+\(([+-])\)\s+\|\s+(\S+)\s+\|\s+(\S+)\s+\|\s+(\S+)/;
 167     my $feat = Bio::SeqFeature::Generic->new(
 168         -seq_id => $self->{found_seq_id},
 169         -start  => $start,
 170         -end    => $start + length($seq) - 1,
 171         -strand => 1,
 172         -score  => $core_score,
 173         -source => 'transfac_match');
 174
 175     my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
 176     $feat->annotation->add_Annotation($sv);
 177     $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_score', -value => $matrix_score);
 178     $feat->annotation->add_Annotation($sv);
 179     $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_id', -value => $matrix_id);
 180     $feat->annotation->add_Annotation($sv);
 181
 182     return $feat;
 183 }
 184
 185 1;