1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
|
package Bio::Tools::PSort::Module::Rules;
# 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::Module::OutputI;
use Bio::Tools::PSort::Report::Result;
use Data::Dumper;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module::OutputI);
use strict;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
sub run {
my ($self, $seq, %res) = @_;
my ($hassig);
# Return HMMTOP prediction if one was made.
if(defined($res{HMMTOP}) && (my ($hmmtop) = @{$res{HMMTOP}})) {
$hassig = 1 if(join('', $hmmtop->details) =~ /signal peptide/i);
return $hmmtop if($hmmtop->localization ne "Unknown");
}
# Return Motif prediction if one was made.
if(defined($res{Motif}) && (my ($motif) = @{$res{Motif}})) {
return $motif if($motif->localization ne "Unknown");
}
# Return OMPMotif prediction if one was made.
if(defined($res{OMPMotif}) && (my ($omotif) = @{$res{OMPMotif}})) {
return $omotif if($omotif->localization ne "Unknown");
}
# Return SCLBlast prediction if one was made.
if(defined($res{SCLBlast}) && (my ($scl) = @{$res{SCLBlast}})) {
return $scl if($scl->localization ne "Unknown");
}
# Check to see if the Signal module found a signal peptide.
if(defined($res{Signal}) && (my ($signal) = @{$res{Signal}})) {
$hassig = 1 if(join('', $signal->details) =~ /signal peptide/i);
}
# Return SubLoc prediction only if Cytoplasmic was predicted.
if(defined($res{SubLoc}) && (my ($subloc) = @{$res{SubLoc}})) {
return $subloc if(($subloc->localization eq "Cytoplasmic") && ! $hassig);
}
return new Bio::Tools::PSort::Report::Result(-loc => 'Unknown');
}
1;
|
