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
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
|
package Bio::Tools::PSort::Module::ModHMM;
# 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::AnalysisI;
use Bio::Tools::PSort::Report::Result;
use Bio::Tools::PSort::ModHMM;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module::AnalysisI);
use strict;
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($hmmfile, $repfile, $path, $loc, $cutoff) = $self->_rearrange([ qw(HMMFILE REPFILE PATH LOC CUTOFF) ], @args);
$self->throw("No localization specified in ModHMM\n") if(!$loc);
$self->{loc} = $loc;
$self->throw("No HMM file specified in ModHMM\n") if(!$hmmfile);
$self->{hmmfile} = $hmmfile;
$self->throw("No replacement letter file specified in ModHMM\n") if(!$repfile);
$self->{repfile} = $repfile;
$self->throw("Path specified in ModHMM\n") if(!$path);
$self->{path} = $path;
# 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 $rep = getHelices($seq->seq, $self->{hmmfile}, $self->{repfile}, $self->{path});
my $num = $rep->count;
$self->throw("Error openning HMM file in ModHMM\n") if($num == -10);
$self->throw("Error openning replacement letter file in ModHMM\n") if($num == -11);
$self->throw("Error with sequence in ModHMM\n") if($num == -12);
$self->throw("Error with ModHMM path\n") if($num == -13);
# 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(my $i=1;$i <= $rep->count; $i++) {
$num-- if($rep->end($i) <= 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;
|
