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package Bio::Tools::Run::SCLBlastLocal;
# 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::Run::SCLBlast::Report;
use Bio::Tools::Run::SCLBlast::Hit;
use Bio::SearchIO;
use Bio::Search::HSP::BlastHSP;
use Bio::Root::Root;
use File::Temp qw/ tempfile /;
use strict;
our @ISA = qw(Bio::Root::Root);
our $VERSION = '0.02';
our %ENV;
sub new {
my ($class, %args) = @_;
my $self = bless {
exact => $args{-exact} || 0,
-database => $args{-database} || '',
-blastdir => $args{-blastdir} || '',
blastbin => $args{-blastbin} || '',
}, $class;
$self->throw("Failed to initialize SCLBlastLocal, $self->{blastbin} not executable")
if($self->{blastbin} && (! -x $self->{blastbin}));
$self->{parser} = sub {
my $line = shift;
# Extract the localization/description strings.
# $line =~ /^.*\[(.*)\]\s+(.*)$/;
# $line =~ /^\s*\[(\S+)\]\s+(.*)$/;
$line =~ /^\s*\[(\S+)\]\s*(\[\S+\])?\s+(.*)$/;
my ($loc, $sec, $dsc) = ($1, $2, $3);
# Check to see if we have multiple localizations.
$loc = [split(/\s+|\,/, $loc)] if($loc =~ /\,/);
# Check to see if we have secondary localizations
my $secloc = [];
if($sec) {
$sec =~ /\[(\S+)\]/;
$secloc = $1;
$secloc = [split(/\s+|\,/, $secloc)] if($secloc =~ /\,/);
}
return ($loc, $secloc, $dsc);
};
return $self;
}
sub parser {
my ($self, $parser) = @_;
$self->throw("Not a CODE reference") if(ref($parser) ne "CODE");
$self->{parser} = $parser;
}
sub blast {
my ($self, $seq) = @_;
my ($blast, $brep);
my $qper;
my $hper;
my $fracID;
my $expect;
# Ensure we received a Bio::Seq object.
$self->throw("Not a Bio::Seq object")
if((! ref($seq)) || (! $seq->isa('Bio::Seq')));
# Get temp file for blast report
my ($repfh, $repfile) = tempfile();
open(BLAST, "|$self->{blastbin} -p blastp -d $self->{-database} -F F -e 1e-02 -o $repfile");
print BLAST $seq->seq;
close BLAST;
my $brep = new Bio::SearchIO(-format => 'blast', -file => "$repfile");
# Blast the sequence.
# $brep = $self->{blast}->blastall($seq);
# $self->{blast}->cleanup;
return () if(! $brep);
my $bres = $brep->next_result();
# Create a list of the hits on the sequence.
my @hits = ();
while(my $hit = $bres->next_hit()) {
my @hsps;
while(my $hsp = $hit->next_hsp) {
$qper = $hsp->length('hit')/$hsp->length('query') * 100;
$expect = $hsp->evalue();
# Check the evalue to make sure it's in range (stupid Blast bug)
next if($expect > 1e-9);
# If we're in exact match mode, skip those not within 1 basepairs
# in similar length
next if($self->{exact} && (abs($hit->length() - $seq->length()) > 1));
# Add the HSP to the list if it meets our length criteria.
push(@hsps, $hsp) if(($qper > 80) && ($qper < 120));
$fracID = $hsp->frac_identical('total')*100;
}
if(@hsps) {
my ($loc, $secloc, $desc) = $self->{parser}->($hit->description);
if(!(($self->{exact}) && !( $qper == 100 && $fracID == 100))) {
my $hit = new Bio::Tools::Run::SCLBlast::Hit(
'-localization' => $loc,
'-secondloc' => $secloc,
'-description' => ($self->{exact}?'100% ':'') . $hit->name . ": " . $desc,
'-algorithm' => 'blastp',
'-name' => 'sclblast',
'-length' => $hit->length,
'-hsps' => \@hsps);
push(@hits, $hit);
}
}
}
# Explicitly close and unlink the temp file to make sure it gets erased
close $repfh;
unlink $repfile;
return new Bio::Tools::Run::SCLBlast::Report(-hits => \@hits);
}
1;
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