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package Bio::Tools::Signal::Report;
# 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::Root::Root;
use strict;
our @ISA = qw(Bio::Root::Root);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
sub cleavage_site {
my $self = shift;
return (@_) ? $self->{csite} = shift : $self->{csite};
}
sub is_lipoprotein {
my $self = shift;
return (@_) ? $self->{islipo} = shift : $self->{islipo};
}
sub localization {
my $self = shift;
return (@_) ? $self->{loc} = shift : $self->{loc};
}
sub hmm_score {
my $self = shift;
return (@_) ? $self->{hmmscore} = shift : $self->{hmmscore};
}
sub hmm_pvalue {
my $self = shift;
return (@_) ? $self->{hmmpvalue} = shift : $self->{hmmpvalue};
}
sub svm_prediction {
my $self = shift;
return (@_) ? $self->{svmpred} = shift : $self->{svmpred};
}
sub signal_peptide {
my $self = shift;
return ($self->{islipo} || ($self->{hmmpvalue} < 0.01) ||
(($self->{hmmpvalue} < 0.05) && $self->{svmpred})) ? 1 : 0;
}
1;
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