|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
|
|
|
4 Genome Research Limited. All rights reserved.
|
|
|
5
|
|
|
6 This software is distributed under a modified Apache license.
|
|
|
7 For license details, please see
|
|
|
8
|
|
|
9 http://www.ensembl.org/info/about/code_licence.html
|
|
|
10
|
|
|
11 =head1 CONTACT
|
|
|
12
|
|
|
13 Please email comments or questions to the public Ensembl
|
|
|
14 developers list at <dev@ensembl.org>.
|
|
|
15
|
|
|
16 Questions may also be sent to the Ensembl help desk at
|
|
|
17 <helpdesk@ensembl.org>.
|
|
|
18
|
|
|
19 =cut
|
|
|
20
|
|
|
21 =head1 NAME
|
|
|
22
|
|
|
23 Bio::EnsEMBL::RepeatFeature - A feature representing a repeat on a piece of
|
|
|
24 sequence.
|
|
|
25
|
|
|
26 =head1 SYNOPSIS
|
|
|
27
|
|
|
28 my $rf = new Bio::EnsEMBL::Feature(
|
|
|
29 -start => 100,
|
|
|
30 -end => 220,
|
|
|
31 -strand => -1,
|
|
|
32 -slice => $slice,
|
|
|
33 -analysis => $analysis,
|
|
|
34 -repeat_consensus => $rc,
|
|
|
35 -hstart => 10,
|
|
|
36 -hend => 100,
|
|
|
37 -hstrand => 1,
|
|
|
38 -score => 83.2
|
|
|
39 );
|
|
|
40
|
|
|
41 my $hstart = $feat->hstart;
|
|
|
42 my $hend = $feat->hend;
|
|
|
43
|
|
|
44 # move the feature to the chromosomal coordinate system
|
|
|
45 $feature = $feature->transform('chromosome');
|
|
|
46
|
|
|
47 # move the feature to a different slice
|
|
|
48 # (possibly on another coord system)
|
|
|
49 $feature = $feature->transfer($new_slice);
|
|
|
50
|
|
|
51 # project the feature onto another coordinate system possibly across
|
|
|
52 # boundaries:
|
|
|
53 @projection = @{ $feature->project('contig') };
|
|
|
54
|
|
|
55 # change the start, end, and strand of the feature in place
|
|
|
56 $feature->move( $new_start, $new_end, $new_strand );
|
|
|
57
|
|
|
58 =head1 DESCRIPTION
|
|
|
59
|
|
|
60 This a feature representing a repeat region on a sequence
|
|
|
61
|
|
|
62 =head1 METHODS
|
|
|
63
|
|
|
64 =cut
|
|
|
65
|
|
|
66 package Bio::EnsEMBL::RepeatFeature;
|
|
|
67
|
|
|
68 use strict;
|
|
|
69
|
|
|
70 use Bio::EnsEMBL::Utils::Exception qw(throw);
|
|
|
71 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
|
|
|
72
|
|
|
73 use base qw/Bio::EnsEMBL::Feature/;
|
|
|
74
|
|
|
75 =head2 new
|
|
|
76
|
|
|
77 Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
|
|
|
78 The repeat consensus for this repeat feature
|
|
|
79 Arg [HSTART] : int (optional)
|
|
|
80 The hit start on the consensus sequence
|
|
|
81 Arg [HEND] : int (optional)
|
|
|
82 The hit end on the consensus sequence
|
|
|
83 Arg [SCORE] : float (optional)
|
|
|
84 The score
|
|
|
85 Arg [...] : Named arguments to superclass constructor
|
|
|
86 (see Bio::EnsEMBL::Feaure)
|
|
|
87 Example : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
|
|
|
88 -HSTART => 10,
|
|
|
89 -HEND => 100,
|
|
|
90 -SCORE => 58.0,
|
|
|
91 -START => 1_000_100,
|
|
|
92 -END => 1_000_190,
|
|
|
93 -STRAND => 1,
|
|
|
94 -ANALYSIS => $an,
|
|
|
95 -SLICE => $chr_slice);
|
|
|
96 Description: Creates a new Bio::EnsEMBL::RepeatFeature object
|
|
|
97 Returntype : Bio::EnsEMBL::RepeatFeature
|
|
|
98 Exceptions : none
|
|
|
99 Caller : RepeatFeatureAdaptors
|
|
|
100 Status : Stable
|
|
|
101
|
|
|
102 =cut
|
|
|
103
|
|
|
104 sub new {
|
|
|
105 my $caller = shift;
|
|
|
106
|
|
|
107 my $class = ref($caller) || $caller;
|
|
|
108
|
|
|
109 my $self = $class->SUPER::new(@_);
|
|
|
110
|
|
|
111 my ($repeat_consensus, $hstart, $hend, $score) =
|
|
|
112 rearrange(['REPEAT_CONSENSUS','HSTART','HEND','SCORE'], @_);
|
|
|
113
|
|
|
114 $self->repeat_consensus($repeat_consensus);
|
|
|
115 $self->{'hstart'} = $hstart;
|
|
|
116 $self->{'hend'} = $hend;
|
|
|
117 $self->{'score'} = $score;
|
|
|
118
|
|
|
119 return $self;
|
|
|
120 }
|
|
|
121
|
|
|
122
|
|
|
123 =head2 repeat_consensus
|
|
|
124
|
|
|
125 Arg [1] : (optional) Bio::EnsEMBL::RepeatConsensus
|
|
|
126 Example : $repeat_consensus = $repeat->repeat_consensus;
|
|
|
127 Description: Getter/Setter for the repeat consensus of this repeat
|
|
|
128 Returntype : Bio::EnsEMBL::RepeatConsensus
|
|
|
129 Exceptions : none
|
|
|
130 Caller : general
|
|
|
131 Status : Stable
|
|
|
132
|
|
|
133 =cut
|
|
|
134
|
|
|
135 sub repeat_consensus {
|
|
|
136 my $self = shift;
|
|
|
137
|
|
|
138 if(@_) {
|
|
|
139 my $rc = shift;
|
|
|
140 if(defined($rc)) {
|
|
|
141 if(!ref($rc) || !$rc->isa('Bio::EnsEMBL::RepeatConsensus')) {
|
|
|
142 throw('RepeatConsensus arg must be a Bio::EnsEMBL::RepeatConsensus');
|
|
|
143 }
|
|
|
144 }
|
|
|
145 $self->{'repeat_consensus'} = $rc;
|
|
|
146 }
|
|
|
147
|
|
|
148 return $self->{'repeat_consensus'};
|
|
|
149 }
|
|
|
150
|
|
|
151
|
|
|
152
|
|
|
153 =head2 hstart
|
|
|
154
|
|
|
155 Arg [1] : (optional) int $hstart
|
|
|
156 Example : $hit_start = $repeat->hstart;
|
|
|
157 Description: Getter/Setter for the start bp of this repeat match on the
|
|
|
158 consensus sequence.
|
|
|
159 Returntype : int
|
|
|
160 Exceptions : none
|
|
|
161 Caller : general
|
|
|
162 Status : Stable
|
|
|
163
|
|
|
164 =cut
|
|
|
165
|
|
|
166 sub hstart {
|
|
|
167 my $self = shift;
|
|
|
168 $self->{'hstart'} = shift if(@_);
|
|
|
169 return $self->{'hstart'};
|
|
|
170 }
|
|
|
171
|
|
|
172
|
|
|
173 =head2 score
|
|
|
174
|
|
|
175 Arg [1] : (optional) float $score
|
|
|
176 Example : $score = $repeat->score();
|
|
|
177 Description: Getter/Setter for the score of this repeat feature
|
|
|
178 Returntype : int
|
|
|
179 Exceptions : none
|
|
|
180 Caller : general
|
|
|
181 Status : Stable
|
|
|
182
|
|
|
183 =cut
|
|
|
184
|
|
|
185 sub score {
|
|
|
186 my $self = shift;
|
|
|
187 $self->{'score'} = shift if(@_);
|
|
|
188 return $self->{'score'};
|
|
|
189 }
|
|
|
190
|
|
|
191
|
|
|
192
|
|
|
193 =head2 hend
|
|
|
194
|
|
|
195 Arg [1] : (optional) int $hend
|
|
|
196 Example : $hit_end = $repeat->hend;
|
|
|
197 Description: Getter/Setter for the end bp of this repeat match on the
|
|
|
198 consensus sequence.
|
|
|
199 Returntype : int
|
|
|
200 Exceptions : none
|
|
|
201 Caller : general
|
|
|
202 Status : Stable
|
|
|
203
|
|
|
204 =cut
|
|
|
205
|
|
|
206 sub hend {
|
|
|
207 my $self = shift;
|
|
|
208 $self->{'hend'} = shift if(@_);
|
|
|
209 return $self->{'hend'};
|
|
|
210 }
|
|
|
211
|
|
|
212
|
|
|
213
|
|
|
214 =head2 hstrand
|
|
|
215
|
|
|
216 Arg [1] : none
|
|
|
217 Example : none
|
|
|
218 Description: always returns 1. method exists for consistancy with other
|
|
|
219 features.
|
|
|
220 Returntype : int
|
|
|
221 Exceptions : none
|
|
|
222 Caller : general
|
|
|
223 Status : Stable
|
|
|
224
|
|
|
225 =cut
|
|
|
226
|
|
|
227 sub hstrand {
|
|
|
228 return 1;
|
|
|
229 }
|
|
|
230
|
|
|
231
|
|
|
232 =head2 display_id
|
|
|
233
|
|
|
234 Arg [1] : none
|
|
|
235 Example : print $rf->display_id();
|
|
|
236 Description: This method returns a string that is considered to be
|
|
|
237 the 'display' identifier. For repeat_features this is the
|
|
|
238 name of the repeat consensus if it is available otherwise it is
|
|
|
239 an empty string.
|
|
|
240 Returntype : string
|
|
|
241 Exceptions : none
|
|
|
242 Caller : web drawing code
|
|
|
243 Status : Stable
|
|
|
244
|
|
|
245 =cut
|
|
|
246
|
|
|
247 sub display_id {
|
|
|
248 my $self = shift;
|
|
|
249
|
|
|
250 my $id = '';
|
|
|
251
|
|
|
252 my $rc = $self->{'repeat_consensus'};
|
|
|
253 if($rc) {
|
|
|
254 $id = $rc->name();
|
|
|
255 }
|
|
|
256
|
|
|
257 return $id;
|
|
|
258 }
|
|
|
259
|
|
|
260
|
|
|
261 1;
|
|
|
262
|
|
|
263 __END__
|
|
|
264
|
|
|
265 =head1 NAME - Bio::EnsEMBL::RepeatFeature
|
|
|
266
|
|
|
267 =head1 AUTHOR
|
|
|
268
|
|
|
269 James Gilbert B<email> jgrg@sanger.ac.uk
|
|
|
270
|
