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package Bio::Tools::PSort::Module::SCLBlast;
# 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::Report::Result;
use Bio::Tools::PSort::Constants qw(:all);
use Bio::Tools::PSort::Module::AnalysisI;
use Bio::Tools::Run::SCLBlast;
use Bio::Tools::Run::SCLBlastLocal;
use Bio::SearchIO;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($db, $exact, $blastbin) = $self->_rearrange([qw(DATABASE EXACT BLASTBIN)], @args);
# Save the parameters for the reload option
$self->{db} = $db;
$self->{exact} = $exact;
$self->{blastbin} = $blastbin;
# Create a new Bio::Tools::Run::SBLBlast instance.
if($blastbin) {
$self->{sclblast} = new Bio::Tools::Run::SCLBlastLocal( -database => $db, -exact => $exact, -blastbin => $blastbin );
} else {
$self->{sclblast} = new Bio::Tools::Run::SCLBlast( -database => $db, -exact => $exact );
}
return $self;
}
sub run {
my ($self, $seq) = @_;
my @res;
# Ensure that we received a Bio::Seq object.
$self->throw("Didn't receive a Bio::Seq")
if((! ref($seq)) || (! $seq->isa('Bio::Seq')));
if(my $brep = $self->{sclblast}->blast($seq)) {
my $hit = $brep->next_hit;
if($hit) {
my @locs = $hit->localization;
my @seclocs = $hit->secondarylocalization;
my $r = new Bio::Tools::PSort::Report::Result();
$r->localization(\@locs);
$r->secondarylocalization(\@seclocs);
$r->details(["matched " . $hit->description]);
push(@res, $r);
}
}
@res ? @res : new Bio::Tools::PSort::Report::Result(-loc => 'Unknown',
-details => ['No matches against database']);
}
1;
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