Bio::Tools Match
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Match - Parses output from Transfac's match(TM)
Package variables
No package variables defined.
Included modules
Bio::Annotation::SimpleValue
Bio::SeqFeature::Annotated
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
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : $result = $obj->next_result();
Function: Returns the next result available from the input, or undef if there
are no more results.
Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
for 'matrix_score', 'matrix_id' and a 'predicted' tag.
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_initialize_io(@args);
    
    return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    
    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
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 - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _