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package Bio::Tools::PSort::Module::OMPMotif;
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# OVERVIEW
# PSORT-B is described in Gardy, J.L. et al (2003). PSORT-B:
# improving protein subcellular localization prediction for
# Gram-negative bacteria. Nuc Acids Res 31(13):3613-17. Please
# cite this publication if you use PSORT-B in your research.
# The standalone version of PSORT-B is distributed under the GNU
# General Public Licence (Gnu GPL) (see the LICENSE file included
# in the download) by the Brinkman Laboratory, Simon Fraser
# University, Burnaby, B.C., Canada.
# This standalone version of PSORT-B has initially been developed
# for the Linux environment.
# This document describes the installation of the PSORT-B version
# 1.1.4 command line program and the PSORT-B server packages. For
# most purposes, following the installation instructions for the
# command line version will be sufficient.
# For further information, please contact psort-mail@sfu.ca.
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use Bio::Tools::Motif;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
use strict;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($db, $cutoff) = $self->_rearrange([qw(DATABASE CUTOFF)], @args);
$self->{motif} = new Bio::Tools::Motif(-database => $db) ||
$self->throw("Couldn't create new Bio::Tools::Motif object");
# Set the number of patterns needed to make a classification, or default
# to three if a value wasn't provided.
$self->{cutoff} = defined($cutoff) ? ($cutoff + 0) : 3;
return $self;
}
sub run {
my ($self, $seq) = @_;
my @matches = $self->{motif}->match($seq);
if(@matches >= $self->{cutoff}) {
my $detail = "matched " . @matches . " rules";
$detail .= " (" . join(', ', map { $_->motif_id } @matches) . ")";
return new Bio::Tools::PSort::Report::Result(-details => [ $detail ],
-score => 0,
-loc => 'OuterMembrane');
}
return new Bio::Tools::PSort::Report::Result(-loc => 'Unknown',
-details => ['No motifs found']);
}
1;
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONSTRUCTOR
=head1 METHODS
=head1 SEE ALSO
=head1 AUTHOR
Cory Spencer <cspencer@sfu.ca>
=cut
__END__
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