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Summary

Bio::Tools::Match - Parses output from Transfac's match(TM)

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

  use strict;

  use Bio::Tools::Match;

  my $parser = Bio::Tools::Match->new(-file => "match.out");
  
  while (my $feat = $parser->next_result) {
    my $start = $feat->start;
    my $end = $feat->end;
    my $core_score = $feat->score;
    my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
    my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
  }

Description

This module is used to parse the output from Transfac's match(TM) program. It
doesn't support the histogram output of match.
Each result is a Bio::SeqFeature::Annotated representing a single matrix match.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Tools::Match->new();
 Function: Builds a new Bio::Tools::Match object
 Returns : Bio::Tools::Match
 Args    : -file (or -fh) should contain the contents of a standard match output

 Title   : next_result
 Usage   : $result = $obj->next_result();
 Function: Returns the next result available from the input, or undef if there
           are no more results.
 Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
           for 'matrix_score', 'matrix_id' and a 'predicted' tag.
 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) = @_;
    
    my $line = $self->_readline || return;
    
    if (! $self->{found_seq_id} && $line =~ /^Inspecting sequence ID\s+(.+)/) {
        $self->{found_seq_id} = $1;
    }
    
    while ($line !~ /^\s\S+\s+\|\s+\d+/) {
        $line = $self->_readline || return;
    }
    
    
    # The first column gives the TRANSFAC(r) identifier of the matching matrix,
    # then comes the position and the strand where the respective match has been
    # found. The core similarity score is given in column three, the matrix
    # similarity score in column four. The last column gives the matching
    # sequence.
    #
    #
    #Search for sites by WeightMatrix library: /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat
    #Sequence file: sequence.fa
    #Site selection profile: mxprf Profile generated from /home/sendu/files/programs/transfac/cgi-bin/data/matrix.dat with default values.
    #
    #
    #Inspecting sequence ID   Homo_sapiens
    #
    # V$MYOD_01              |        5 (+) |  0.751 |  0.784 | ttaGAGGTggcg
    # V$MYOD_01              |        5 (-) |  0.778 |  0.580 | ttagAGGTGgcg
    # V$MYOD_01              |       30 (+) |  0.751 |  0.581 | gctCAGGCaccc
    #[...]
    # V$RORA_Q4              |    53610 (+) |  0.775 |  0.668 | tgtgggGGCCA
    # V$RORA_Q4              |    53639 (+) |  0.775 |  0.636 | gtcgggGGACA
    #
    # Total sequences length=53654
    #
    # Total number of found sites=1735559
    #
    # Frequency of sites per nucleotide=32.347243
    
    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+)/;
    my $feat = Bio::SeqFeature::Annotated->new(
        -seq_id => $self->{found_seq_id},
        -start  => $start, 
        -end    => $start + length($seq) - 1,
        -strand => 1,
        -score  => $core_score,
        -source => 'transfac_match');
    
    my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
    $feat->annotation->add_Annotation($sv);
    $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_score', -value => $matrix_score);
    $feat->annotation->add_Annotation($sv);
    $sv = Bio::Annotation::SimpleValue->new(-tagname => 'matrix_id', -value => $matrix_id);
    $feat->annotation->add_Annotation($sv);
    
    return $feat;
}

1;

}

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

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.

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/

Email bix@sendu.me.uk

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