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
180
181
182
183
184
185
186
187
188
189
190
191
192
193
|
# $Id: TranscriptionFactor.pm,v 1.6 2006/07/17 14:16:53 sendu Exp $
#
# BioPerl module for Bio::Map::TranscriptionFactor
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable
element
=head1 SYNOPSIS
use Bio::Map::TranscriptionFactor;
use Bio::Map::GeneMap;
use Bio::Map::Position;
# model a TF that binds 500bp upstream of the BRCA2 gene in humans and
# 250bp upstream of BRCA2 in mice
my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
my $map1 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
-species => "human");
my $map2 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
-species => "mouse");
Bio::Map::Position->new(-map => $map1,
-element => $tf,
-start => -500,
-length => 10);
Bio::Map::Position->new(-map => $map2,
-element => $tf,
-start => -250,
-length => 10);
# Find out where the transcription factor binds
foreach $pos ($tf->get_positions) {
print $tf->universal_name, " binds at position " $pos->value, " relative to ",
$pos->relative->description, " of gene ",
$pos->map->universal_name, " in species ", $pos->map->species, "\n";
}
=head1 DESCRIPTION
A transcription factor modelled as a mappable element. It can have mulitple
binding sites (positions) near multiple genes (maps).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Map::TranscriptionFactor;
use strict;
use base qw(Bio::Map::Mappable);
our $TFS = {};
=head2 new
Title : new
Usage : my $tf = Bio::Map::TranscriptionFactor->new();
Function: Builds a new Bio::Map::TranscriptionFactor object
Returns : Bio::Map::TranscriptionFactor
Args : -universal_name => string name of the TF (in a form common to all
species that have the TF, but unique amongst
non-orthologous TFs), REQUIRED
-description => string, free text description of the TF
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($u_name, $desc) = $self->_rearrange([qw(UNIVERSAL_NAME DESCRIPTION)], @args);
$u_name || $self->throw("You must supply a -universal_name");
$self->universal_name($u_name);
defined $desc && $self->description($desc);
return $self;
}
=head2 get
Title : get
Usage : my $obj = Bio::Map::TranscriptionFactor->get();
Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or
gets a pre-existing one that shares the same universal_name.
Returns : Bio::Map::TranscriptionFactor
Args : -universal_name => string name of the TF (in a form common to all
species that have the TF, but unique amongst
non-orthologous TFs), REQUIRED
-description => string, free text description of the TF
=cut
sub get {
my ($class, @args) = @_;
my ($u_name) = Bio::Root::Root->_rearrange([qw(UNIVERSAL_NAME)], @args);
if ($u_name && defined $TFS->{$u_name}) {
return $TFS->{$u_name};
}
return $class->new(@args);
}
=head2 universal_name
Title : universal_name
Usage : my $name = $obj->universal_name
Function: Get/Set TF name, corresponding to the name of the TF in a form shared
by orthologous versions of the TF in different species, but otherwise
unique.
Returns : string
Args : none to get, OR string to set
=cut
sub universal_name {
my ($self, $value) = @_;
if (defined $value) {
delete $TFS->{$self->{'_uname'}} if $self->{'_uname'};
$self->{'_uname'} = $value;
$TFS->{$value} = $self;
}
return $self->{'_uname'};
}
=head2 description
Title : description
Usage : my $desc = $obj->description
Function: Get/Set a description of the TF.
Returns : string
Args : none to get, OR string to set
=cut
sub description {
my $self = shift;
if (@_) { $self->{desc} = shift }
return $self->{desc} || '';
}
1;
|
