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package Bio::Tools::PSort::Module::HMMTOP;
# 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 Bio::Tools::Run::HMMTOP;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
# The hmmtop processes have a habit of going zombie without this.
$SIG{CHLD} = 'IGNORE';
use strict;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($dir, $loc, $cutoff) = $self->_rearrange([ qw(HMMTOPDIR LOC CUTOFF) ], @args);
$self->{hmmtop} = new Bio::Tools::Run::HMMTOP(-hmmtopdir => $dir) ||
$self->throw("Couldn't create new Bio::Tools::HMMTOP object");
$self->throw("No localization specified in HMMTOP\n") if(!$loc);
$self->{loc} = $loc;
# Set the number of helices we expect for an CytoplasmicMembrane protein.
$self->{cutoff} = (defined($cutoff) ? ($cutoff + 0) : 3);
return $self;
}
sub run {
my ($self, $seq, %prev) = @_;
# Ensure we received a Bio::Seq object.
$self->throw("Not a Bio::Seq object")
if((! ref($seq)) && (! $seq->isa("Bio::Seq")));
my $rep = $self->{hmmtop}->analyze($seq);
my $num = $rep->num_helices;
# Check to see if we have data from the Signal module - if we do, we should
# reduce the helix count IF a signal peptide was detected and a TMH was found
# before amino acid 70.
if(exists($prev{Signal})) {
my ($res) = @{$prev{Signal}};
if($res->details =~ /^Signal peptide detected/) {
for(rep->num_helices) {
$num-- if($_->end <= 70);
}
}
}
my $details;
SWITCH: {
($num == 0) && do {
$details = "No internal helices found";
last SWITCH;
};
($num == 1) && do {
$details = "1 internal helix found";
last SWITCH;
};
$details = "$num internal helices found";
};
if($num >= $self->{cutoff}) {
return new Bio::Tools::PSort::Report::Result(-details => [ $details ],
-score => 0,
-loc => $self->{loc});
} else {
return new Bio::Tools::PSort::Report::Result(-details => [ $details ],
-score => 0,
-loc => 'Unknown');
}
}
1;
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