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
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
|
package Bio::Tools::PSort::Profile;
use Bio::Tools::PSort::Profile::Match;
use Bio::SeqIO;
use Bio::Root::IO;
use Bio::Root::Root;
use Carp;
use strict;
our @ISA = qw(Bio::Root::Root);
our $VERSION = '0.01';
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# Get the file paths for the profile and for the pfscan binary
my ($profiledb, $pfscan, $profileids) =
$self->_rearrange([qw(DATABASE PROGRAM PROFILEIDS)], @args);
$self->throw("No profile database selected") if (!$profiledb);
$self->{profile}->{profiledb} = $profiledb;
$self->throw("No pfscan path selected") if (!$pfscan);
$self->{profile}->{pfscan} = $pfscan;
$self->throw("No profile ids file selected") if (!$profileids);
#this file contains a the profile_ids and the corresponding localization
open(PROFILEIDS, $profileids) or $self->throw("Could not open file $profileids");
###build a hash with ids as keys and scl's as values
my %localization;
while(<PROFILEIDS>){
if (/^(\S+)\s+(\S+)/){
my $id = $1;
my $scl = $2; #'
chomp($scl);
$localization{$id} = $scl;
}
}
close PROFILEIDS;
$self->{profile}->{profileids} = \%localization;
return $self;
}
sub match {
my ($self, $seq) = @_; ### we need to PASS IN THE PROFILE DB NAME SOMEHOW!!
my @matches = ( );
# Make sure that we received a sequence object.
$self->throw("Not a Bio::Seq object")
if((! ref($seq)) || (! $seq->isa("Bio::SeqI")));
my $pf = $self->{profile}->{pfscan};
my $profiles = $self->{profile}->{profiledb};
my %localization = %{$self->{profile}->{profileids}};
# Make a temp file for the sequence
my $io = new Bio::Root::IO;
my($fh, $tempfile) = $io->tempfile();
my $out = Bio::SeqIO->new(-fh => $fh, -format => 'fasta');
$out->write_seq($seq);
$out->close();
close($fh);
# Open pfscan and use it as a filter
open(RESULTS, "$pf -f $tempfile $profiles |") || $self->throw("Can't load pfscan: $!");
# Read the results of pfscan
my @seq = <RESULTS>;
close RESULTS;
#must parse the output
#score number pos. x - y PROSITE_ID|DESCRIPTION
# Is there any output from pfscan?
if ($#seq >= 0) {
# break each line down and extract what we need
foreach my $line (@seq) {
if($line=~/^\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+\-\s+(\d+)\s+(\S+)\|/) {
my $score = $1;
my $num = $2;
my $pos = $3;
my $start = $4;
my $end = $5;
my $profile_id = $6;
my $desc = $'; #'
chomp ($desc);
=pod
my %localization = ( PS50253 => "CytoplasmicMembrane", PS50283 => "CytoplasmicMembrane", PS50830 => "Extracellular", PS50847 => "Cell Wall", PS50850 => "CytoplasmicMembrane", PS50862 => "Cytoplasmic");
=cut
my $m = new Bio::Tools::PSort::Profile::Match(-profileid => $profile_id,
-localization => $localization{$profile_id},
-comment => $desc,
-start => $start,
-end => $end);
push(@matches, $m);
}#end if (regex)
}#end foreach
}#end if
return @matches;
}
=head1 NAME
Bio::Tools::PSort::Profile - Perl implementation of the Profile protein subcellular
localization method.
=head1 SYNOPSIS
use Bio::Tools::PSort::Profile;
# Load a previously trained profile from a file.
$motif = new Bio::Tools::PSort::Profile(-database => 'profile-db.txt');
# Attempt to match on a Bio::Seq object.
@matches = $motif->match($seq);
print($seq->display_id . ": matched " . $_->profile_id . "\n") for(@matches);
=head1 DESCRIPTION
Bio::Tools::Motif uses a selection of motifs that have been identified
to be typical of proteins resident at a specific subcellular localization.
The module accepts a Bio::Seq object and attempts to match it against
a database, returning one or more Bio::Tools::Motif::Match objects with
the prediction information if successful.
=head1 CONSTRUCTOR
$motif = new Bio::Tools::Motif(-database => 'motif-db.txt');
The Motif constructor accepts the name of an existing database file.
=head1 METHODS
@matches = $motif->match($seq);
The match method accepts a Bio::Seq object as an argument and returns
an array of Bio::Tools::Motif::Match objects that matched the given
sequence.
=head1 AUTHOR
Fiona Brinkman, Chris Walsh, Matthew Laird <psort-mail@sfu.ca>
Brinkman Lab, Simon Fraser University, Canada
=head1 SEE ALSO
Bio::Tools::Motif::Pattern, Bio::Tools::Motif::Match
=head1 ACKNOWLEGEMENTS
Thanks go out to Fiona Brinkman, Jennifer Gardy and the other members of the
Simon Fraser University Brinkman laboratory.
=cut
1;
|
