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package Bio::Tools::PSort::Module::Signal;
# 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::Constants qw(:all);
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($svm, $hmm, $prog, $gram) = $self->_rearrange([ qw(SVM HMM PROGRAM GRAM) ], @args);
$self->{svm} = $svm || $self->throw("No SVM model specified.");
$self->{hmm} = $hmm || $self->throw("No HMM model specified.");
$self->{program} = $prog || $self->throw("No signal program specified. ");
$self->{gram} = ($gram eq 'Positive'?1:0);
return $self;
}
sub run {
my ($self, $seq, %prev) = @_;
my ($hassig);
$self->throw("Not a Bio::Seq object")
if((! ref($seq)) && (! $seq->isa("Bio::Seq")));
# Check to see if we can detect a signal peptide with the HMM/SVM module.
my $sq = $seq->seq;
# Run the program to check for signal peptides.
open(SIG, "$self->{program} --svm=$self->{svm} --hmm=$self->{hmm} $sq |");
my $res = <SIG>;
chomp($res);
close(SIG);
$hassig = 1 if($res);
# If a signal peptide was detected the sequence is one of the non-cytoplasmic
# localizations.
if($hassig) {
my @locs;
if($self->{gram}) {
@locs = qw(CytoplasmicMembrane Extracellular Cellwall);
} else {
@locs = qw(CytoplasmicMembrane Periplasmic OuterMembrane Extracellular);
}
my $detail = "Signal peptide detected";
return new Bio::Tools::PSort::Report::Result(-loc => \@locs,
-details => [ $detail ]);
} else {
my $detail = "No signal peptide detected";
return new Bio::Tools::PSort::Report::Result(-loc => "Unknown",
-details => [ $detail ]);
}
}
1;
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