-
Notifications
You must be signed in to change notification settings - Fork 182
/
Intron.pm
303 lines (232 loc) · 8.9 KB
/
Intron.pm
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
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
#
# BioPerl module for Bio::SeqFeature::Gene::Intron
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by David Block <dblock@gene.pbi.nrc.ca>
#
# Copyright David Block
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::Gene::Intron - An intron feature
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - David Block
Email dblock@gene.pbi.nrc.ca
=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::SeqFeature::Gene::Intron;
use strict;
use Bio::SeqFeature::Gene::Exon;
use base qw(Bio::SeqFeature::Gene::NC_Feature);
sub new {
my($class,@args) = @_;
# introns are non-coding by default
if(! grep { lc($_) eq '-is_coding'; } @args) {
push(@args, '-is_coding', 0);
}
my $self = $class->SUPER::new(@args);
my ($primary, $prim) =
$self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
$self->primary_tag('intron') unless $primary || $prim;
return $self;
}
=head2 upstream_Exon
Title : upstream_Exon
Usage : $intron->upstream_Exon()
Function: exon upstream of the intron
Returns : Bio::EnsEMBL::Exon
Args :
=cut
sub upstream_Exon {
my( $self, $exon ) = @_;
if ($exon) {
$self->{'_intron_location'} = undef;
$self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI")
unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
$self->{'_upstream_exon'} = $exon;
}
return $self->{'_upstream_exon'};
}
=head2 downstream_Exon
Title : downstream_Exon
Usage : $intron->downstream_Exon()
Function: exon downstream of the intron
Returns : Bio::EnsEMBL::Exon
Args :
=cut
sub downstream_Exon {
my( $self, $exon ) = @_;
if ($exon) {
$self->{'_intron_location'} = undef;
$self->throw("'$exon' is not a Bio::SeqFeature::Gene::ExonI")
unless $exon->isa('Bio::SeqFeature::Gene::ExonI');
$self->{'_downstream_exon'} = $exon;
}
return $self->{'_downstream_exon'};
}
=head2 phase
Title : phase
Usage : $intron->phase()
Function: returns the phase of the intron(where it interrupts the codon)
Returns : int(0,1,2)
Args :
=cut
sub phase {
my ($self) = @_;
return $self->downstream_Exon->phase;
}
=head2 acceptor_splice_site
Title : acceptor_splice_site
Usage : $intron->acceptor_splice_site(21,3)
Function: returns the sequence corresponding to the
consensus acceptor splice site. If start and
end are provided, it will number of base pairs
left and right of the canonical AG. Here 21 means
21 bp into intron and 3 means 3 bp into the exon.
--Intron--21----|AG|-3-----Exon
Defaults to 21,3
Returns : Bio::Seq
Args : start and end
=cut
sub acceptor_splice_site {
my ($self,$ss_start,$ss_end) = @_;
$ss_start = 21 unless defined $ss_start;
$ss_end = 3 unless defined $ss_end;
if($self->strand < 0){
my $tmp= $ss_start;
$ss_start = $ss_end;
$ss_end = $tmp;
}
my $intron_end= $self->location->end;
my $down_exon = $self->downstream_Exon;
my $acceptor;
if($self->strand < 0){
$ss_start= $ss_start > $down_exon->length ? $down_exon->length: $ss_start;
$ss_end= $ss_end > $self->length-2 ? $self->length-2 : $ss_end;
$acceptor = Bio::SeqFeature::Generic->new(-start=>$self->start - ($ss_start) ,
-end=>$self->start + ($ss_end+1),
-strand=>$self->strand,
-primary_tag=>"donor splice site");
}
else {
$ss_start = $ss_start > $self->length-2 ? $self->length-2 : $ss_start;
$ss_end = $ss_end > $down_exon->length ? $down_exon->length : $ss_end;
$acceptor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start + 1),
-end=>$self->end + $ss_end,
-strand=>$self->strand,
-primary_tag=>"donor splice site");
}
$acceptor->attach_seq($self->entire_seq);
return $acceptor;
}
=head2 donor_splice_site
Title : donor_splice_site
Usage : $intron->donor_splice_site(3,6)
Function: returns the sequence corresponding to the
consensus donor splice site. If start and
end are provided, it will number of base pairs
left and right of the canonical GT. Here 3 means
3 bp into exon and 6 means 6 bp into the intron.
--Exon-3--|GT|-6----Intron-
Defaults to 3,6
Returns : Bio::Seq
Args : start and end
=cut
sub donor_splice_site {
my ($self,$ss_start,$ss_end) = @_;
$ss_start = 3 unless defined $ss_start;
$ss_end = 10 unless defined $ss_end;
if($self->strand < 0){
my $tmp= $ss_start;
$ss_start = $ss_end;
$ss_end = $tmp;
}
my $up_exon = $self->upstream_Exon;
my $donor;
if($self->strand < 0){
$ss_end = $ss_end > $up_exon->length ? $up_exon->length : $ss_end;
$ss_start = $ss_start> $self->length -2 ? $self->length -2 : $ss_start;
$donor = Bio::SeqFeature::Generic->new(-start=>$self->end - ($ss_start+1),
-end => $self->end + ($ss_end),
-strand=>$self->strand,
-primary_tag=>"acceptor splice site");
}
else {
$ss_start = $ss_start > $up_exon->length ? $up_exon->length : $ss_start;
$ss_end = $ss_end > $self->length -2 ? $self->length -2 : $ss_end;
$donor = Bio::SeqFeature::Generic->new(-start=>$self->start - $ss_start,
-end => $self->start +($ss_end+1),
-strand=>$self->strand,
-primary_tag=>"acceptor splice site");
}
$donor->attach_seq($self->entire_seq);
return $donor;
}
sub location {
my( $self ) = @_;
unless ($self->{'_intron_location'}) {
my $loc = Bio::Location::Simple->new;
my $up_exon = $self->upstream_Exon;
my $down_exon = $self->downstream_Exon;
# Get the PrimarySeqs attached to both and check it is the same sequence
my $up_seq = $up_exon ->entire_seq;
my $down_seq = $down_exon->entire_seq;
unless (ref($up_seq) eq ref($down_seq) ) {
$self->throw("upstream and downstream exons are attached to different sequences\n'$up_seq' and '$down_seq'");
}
# Check that the exons are on the same strand. (Do I need to bother?)
my $up_strand = $up_exon ->strand;
my $down_strand = $down_exon->strand;
unless ($up_strand == $down_strand) {
$self->throw("upstream and downstream exons are on different strands "
. "('$up_strand' and '$down_strand')");
}
$loc->strand($up_strand);
# $exon_end is the end of the exon which is 5' of the intron on the genomic sequence.
# $exon_start is the start of the exon which is 3' of the intron on the genomic sequence.
my( $exon_end, $exon_start );
if ($up_strand == 1) {
$exon_end = $up_exon ->end;
$exon_start = $down_exon->start;
} else {
$exon_end = $down_exon->end;
$exon_start = $up_exon ->start;
}
unless ($exon_end < $exon_start) {
$self->throw("Intron gap begins after '$exon_end' and ends before '$exon_start'");
}
$loc->start($exon_end + 1);
$loc->end ($exon_start - 1);
# Attach the sequence and location objects to the intron
$self->{'_intron_location'} = $loc;
}
return $self->{'_intron_location'};
}
1;