line |
bran |
sub |
pod |
code |
1
|
|
|
|
package Sanger::CGP::Vagrent::Data::Annotation; |
2
|
|
|
|
|
3
|
|
|
|
##########LICENCE########## |
4
|
|
|
|
# Copyright (c) 2014 Genome Research Ltd. |
5
|
|
|
|
# |
6
|
|
|
|
# Author: Cancer Genome Project cgpit@sanger.ac.uk |
7
|
|
|
|
# |
8
|
|
|
|
# This file is part of VAGrENT. |
9
|
|
|
|
# |
10
|
|
|
|
# VAGrENT is free software: you can redistribute it and/or modify it under |
11
|
|
|
|
# the terms of the GNU Affero General Public License as published by the Free |
12
|
|
|
|
# Software Foundation; either version 3 of the License, or (at your option) any |
13
|
|
|
|
# later version. |
14
|
|
|
|
# |
15
|
|
|
|
# This program is distributed in the hope that it will be useful, but WITHOUT |
16
|
|
|
|
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
17
|
|
|
|
# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more |
18
|
|
|
|
# details. |
19
|
|
|
|
# |
20
|
|
|
|
# You should have received a copy of the GNU Affero General Public License |
21
|
|
|
|
# along with this program. If not, see <http://www.gnu.org/licenses/>. |
22
|
|
|
|
##########LICENCE########## |
23
|
|
|
|
|
24
|
|
|
|
|
25
|
|
4
|
|
use strict; |
26
|
|
4
|
|
use Data::Dumper; |
27
|
|
4
|
|
use List::Util qw(first); |
28
|
|
4
|
|
use Carp; |
29
|
|
4
|
|
use Const::Fast qw(const); |
30
|
|
|
|
|
31
|
|
4
|
|
use Sanger::CGP::Vagrent qw($VERSION); |
32
|
|
4
|
|
use base qw(Sanger::CGP::Vagrent); |
33
|
|
|
|
|
34
|
|
|
|
# sequence context constant values |
35
|
|
|
|
|
36
|
|
|
|
const my $CDS_ANNOTATION_CONTEXT => 'CDS'; |
37
|
|
|
|
const my $MRNA_ANNOTATION_CONTEXT => 'mRNA'; |
38
|
|
|
|
const my $PROTEIN_ANNOTATION_CONTEXT => 'Protein'; |
39
|
|
|
|
|
40
|
|
|
|
const my @ALL_ANNOTATION_CONTEXT => ($CDS_ANNOTATION_CONTEXT,$MRNA_ANNOTATION_CONTEXT,$PROTEIN_ANNOTATION_CONTEXT); |
41
|
|
|
|
|
42
|
|
|
|
# variation type constant values |
43
|
|
|
|
|
44
|
|
|
|
const my $SUBSTITUTION_ANNOTATION_TYPE => 'Substitution'; |
45
|
|
|
|
const my $DELETION_ANNOTATION_TYPE => 'Deletion'; |
46
|
|
|
|
const my $INSERTION_ANNOTATION_TYPE => 'Insertion'; |
47
|
|
|
|
const my $COMPLEX_ANNOTATION_TYPE => 'Complex'; |
48
|
|
|
|
const my $FRAMESHIFT_ANNOTATION_TYPE => 'FrameShift'; |
49
|
|
|
|
const my $UNKNOWN_ANNOTATION_TYPE => 'Unknown'; |
50
|
|
|
|
|
51
|
|
|
|
const my @ALL_ANNOTATION_TYPES => ($COMPLEX_ANNOTATION_TYPE,$FRAMESHIFT_ANNOTATION_TYPE,$INSERTION_ANNOTATION_TYPE,$DELETION_ANNOTATION_TYPE,$SUBSTITUTION_ANNOTATION_TYPE,$UNKNOWN_ANNOTATION_TYPE); |
52
|
|
|
|
|
53
|
|
|
|
# variation subtype constant values for location data description |
54
|
|
|
|
|
55
|
|
|
|
const my $POSITION_KNOWN_SUBTYPE => 'POS-KNOWN'; |
56
|
|
|
|
const my $POSITION_OFFSET_SUBTYPE => 'POS-OFFSET'; |
57
|
|
|
|
const my $POSITION_OFF_SEQUENCE_SUBTYPE => 'POS-OFFSEQ'; |
58
|
|
|
|
|
59
|
|
|
|
const my @ALL_ANNOTATION_SUBTYPES => ($POSITION_OFF_SEQUENCE_SUBTYPE,$POSITION_OFFSET_SUBTYPE,$POSITION_KNOWN_SUBTYPE); |
60
|
|
|
|
|
61
|
|
|
|
1; |
62
|
|
|
|
|
63
|
|
|
|
sub new { |
64
|
|
1700
|
1
|
my $proto = shift; |
65
|
|
|
|
my $class = ref($proto) || $proto; |
66
|
|
|
|
my $self = {}; |
67
|
|
|
|
bless($self, $class); |
68
|
|
|
|
$self->_init(@_); |
69
|
|
|
|
return $self; |
70
|
|
|
|
} |
71
|
|
|
|
|
72
|
|
|
|
sub _init { |
73
|
|
1700
|
|
my $self = shift; |
74
|
|
|
|
my %vars = @_; |
75
|
|
|
|
foreach my $k(keys(%vars)){ |
76
|
100
|
|
|
if($k eq 'minpos'){ |
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
100
|
|
|
|
|
50
|
|
|
|
77
|
|
|
|
$self->{_minpos} = $vars{minpos}; |
78
|
|
|
|
} elsif($k eq 'minOffset'){ |
79
|
|
|
|
$self->{_minOffset} = $vars{minOffset}; |
80
|
|
|
|
} elsif($k eq 'maxpos'){ |
81
|
|
|
|
$self->{_maxpos} = $vars{maxpos}; |
82
|
|
|
|
} elsif($k eq 'maxOffset'){ |
83
|
|
|
|
$self->{_maxOffset} = $vars{maxOffset}; |
84
|
|
|
|
} elsif($k eq 'wt'){ |
85
|
|
|
|
$self->{_wt} = $vars{wt}; |
86
|
|
|
|
} elsif($k eq 'mt'){ |
87
|
|
|
|
$self->{_mt} = $vars{mt}; |
88
|
|
|
|
} elsif($k eq 'acc'){ |
89
|
|
|
|
$self->{_acc} = $vars{acc}; |
90
|
|
|
|
} elsif($k eq 'accversion'){ |
91
|
|
|
|
$self->{_accversion} = $vars{accversion}; |
92
|
|
|
|
} elsif($k eq 'seqlength'){ |
93
|
|
|
|
$self->{_seqlength} = $vars{seqlength}; |
94
|
|
|
|
} elsif($k eq 'db'){ |
95
|
|
|
|
$self->{_db} = $vars{db}; |
96
|
|
|
|
} elsif($k eq 'dbversion'){ |
97
|
|
|
|
$self->{_dbversion} = $vars{dbversion}; |
98
|
|
|
|
} elsif($k eq 'description'){ |
99
|
|
|
|
$self->{_description} = $vars{description}; |
100
|
|
|
|
} elsif($k eq 'context'){ |
101
|
|
|
|
my $good = undef; |
102
|
|
|
|
foreach my $context(@ALL_ANNOTATION_CONTEXT){ |
103
|
100
|
|
|
if($vars{context} eq $context){ |
104
|
|
|
|
$good = $vars{context}; |
105
|
|
|
|
last; |
106
|
|
|
|
} |
107
|
|
|
|
} |
108
|
50
|
|
|
if(defined($good)){ |
109
|
|
|
|
$self->{_context} = $good; |
110
|
|
|
|
} else { |
111
|
|
|
|
croak('recieved unknown annotation context: '.$vars{context}); |
112
|
|
|
|
} |
113
|
|
|
|
} elsif($k eq 'type'){ |
114
|
|
|
|
my $good = undef; |
115
|
|
|
|
foreach my $type(@ALL_ANNOTATION_TYPES){ |
116
|
100
|
|
|
if($vars{type} eq $type){ |
117
|
|
|
|
$good = $vars{type}; |
118
|
|
|
|
last; |
119
|
|
|
|
} |
120
|
|
|
|
} |
121
|
50
|
|
|
if(defined($good)){ |
122
|
|
|
|
$self->{_type} = $good; |
123
|
|
|
|
} else { |
124
|
|
|
|
croak('recieved unknown annotation type: '.$vars{type}); |
125
|
|
|
|
} |
126
|
|
|
|
} elsif($k eq 'subtype'){ |
127
|
|
|
|
my $good = undef; |
128
|
|
|
|
foreach my $subtype(@ALL_ANNOTATION_SUBTYPES){ |
129
|
100
|
|
|
if($vars{subtype} eq $subtype){ |
130
|
|
|
|
$good = $vars{subtype}; |
131
|
|
|
|
last; |
132
|
|
|
|
} |
133
|
|
|
|
} |
134
|
50
|
|
|
if(defined($good)){ |
135
|
|
|
|
$self->{_subtype} = $good; |
136
|
|
|
|
} else { |
137
|
|
|
|
croak('recieved unknown annotation type: '.$vars{subtype}); |
138
|
|
|
|
} |
139
|
|
|
|
} |
140
|
|
|
|
|
141
|
|
|
|
} |
142
|
|
|
|
} |
143
|
|
|
|
|
144
|
|
|
|
sub getCDSAnnotationContext { |
145
|
|
3324
|
1
|
return $CDS_ANNOTATION_CONTEXT; |
146
|
|
|
|
} |
147
|
|
|
|
|
148
|
|
|
|
sub getmRNAAnnotationContext { |
149
|
|
4455
|
1
|
return $MRNA_ANNOTATION_CONTEXT; |
150
|
|
|
|
} |
151
|
|
|
|
|
152
|
|
|
|
sub getProteinAnnotationContext { |
153
|
|
2141
|
1
|
return $PROTEIN_ANNOTATION_CONTEXT; |
154
|
|
|
|
} |
155
|
|
|
|
|
156
|
|
|
|
sub getSubstitutionAnnotationType { |
157
|
|
308
|
1
|
return $SUBSTITUTION_ANNOTATION_TYPE; |
158
|
|
|
|
} |
159
|
|
|
|
|
160
|
|
|
|
sub getDeletionAnnotationType { |
161
|
|
546
|
1
|
return $DELETION_ANNOTATION_TYPE; |
162
|
|
|
|
} |
163
|
|
|
|
|
164
|
|
|
|
sub getComplexAnnotationType { |
165
|
|
458
|
1
|
return $COMPLEX_ANNOTATION_TYPE; |
166
|
|
|
|
} |
167
|
|
|
|
|
168
|
|
|
|
sub getInsertionAnnotationType { |
169
|
|
374
|
1
|
return $INSERTION_ANNOTATION_TYPE; |
170
|
|
|
|
} |
171
|
|
|
|
|
172
|
|
|
|
sub getFrameShiftAnnotationType { |
173
|
|
40
|
1
|
return $FRAMESHIFT_ANNOTATION_TYPE; |
174
|
|
|
|
} |
175
|
|
|
|
|
176
|
|
|
|
sub getUnknownAnnotationType { |
177
|
|
1674
|
1
|
return $UNKNOWN_ANNOTATION_TYPE; |
178
|
|
|
|
} |
179
|
|
|
|
|
180
|
|
|
|
sub getPositionKnownSubtype { |
181
|
|
478
|
1
|
return $POSITION_KNOWN_SUBTYPE; |
182
|
|
|
|
} |
183
|
|
|
|
|
184
|
|
|
|
sub getPositionOffsetSubtype { |
185
|
|
965
|
1
|
return $POSITION_OFFSET_SUBTYPE; |
186
|
|
|
|
} |
187
|
|
|
|
|
188
|
|
|
|
sub getPositionOffSequenceSubtype { |
189
|
|
1674
|
1
|
return $POSITION_OFF_SEQUENCE_SUBTYPE; |
190
|
|
|
|
} |
191
|
|
|
|
|
192
|
|
|
|
sub getMinPos { |
193
|
|
3910
|
1
|
return shift->{_minpos}; |
194
|
|
|
|
} |
195
|
|
|
|
|
196
|
|
|
|
sub getMaxPos { |
197
|
|
4191
|
1
|
return shift->{_maxpos}; |
198
|
|
|
|
} |
199
|
|
|
|
|
200
|
|
|
|
sub getMinOffset { |
201
|
|
2062
|
1
|
return shift->{_minOffset}; |
202
|
|
|
|
} |
203
|
|
|
|
|
204
|
|
|
|
sub getMaxOffset { |
205
|
|
2034
|
1
|
return shift->{_maxOffset}; |
206
|
|
|
|
} |
207
|
|
|
|
|
208
|
|
|
|
sub getWt { |
209
|
|
1824
|
1
|
return shift->{_wt}; |
210
|
|
|
|
} |
211
|
|
|
|
|
212
|
|
|
|
sub getMt { |
213
|
|
1970
|
1
|
return shift->{_mt}; |
214
|
|
|
|
} |
215
|
|
|
|
|
216
|
|
|
|
sub getDescription { |
217
|
|
1741
|
1
|
return shift->{_description}; |
218
|
|
|
|
} |
219
|
|
|
|
|
220
|
|
|
|
sub getContext { |
221
|
|
13512
|
1
|
return shift->{_context}; |
222
|
|
|
|
} |
223
|
|
|
|
|
224
|
|
|
|
sub getType { |
225
|
|
1700
|
1
|
return shift->{_type}; |
226
|
|
|
|
} |
227
|
|
|
|
|
228
|
|
|
|
sub getSubtype { |
229
|
|
1989
|
1
|
return shift->{_subtype}; |
230
|
|
|
|
} |
231
|
|
|
|
|
232
|
|
|
|
sub getAccession { |
233
|
|
1700
|
1
|
return shift->{_acc}; |
234
|
|
|
|
} |
235
|
|
|
|
|
236
|
|
|
|
sub getSequenceVersion { |
237
|
|
1700
|
1
|
return shift->{_accversion}; |
238
|
|
|
|
} |
239
|
|
|
|
|
240
|
|
|
|
sub getDatabase { |
241
|
|
1700
|
1
|
return shift->{_db}; |
242
|
|
|
|
} |
243
|
|
|
|
|
244
|
|
|
|
sub getDatabaseVersion { |
245
|
|
1700
|
1
|
return shift->{_dbversion}; |
246
|
|
|
|
} |
247
|
|
|
|
|
248
|
|
|
|
sub getSequenceLength { |
249
|
|
0
|
1
|
return shift->{_seqlength}; |
250
|
|
|
|
} |
251
|
|
|
|
|
252
|
|
|
|
sub addClassification { |
253
|
|
2840
|
1
|
my ($self,@classes) = @_; |
254
|
|
|
|
foreach my $c (@classes){ |
255
|
50
|
|
|
if(defined($c)){ |
256
|
100
|
|
|
if(defined($self->getClassifications)){ |
257
|
50
|
1518
|
|
push(@{$self->{_class}},$c) unless(first {$_ eq $c} $self->getClassifications); |
258
|
|
|
|
} else { |
259
|
|
|
|
push(@{$self->{_class}},$c); |
260
|
|
|
|
} |
261
|
|
|
|
} |
262
|
|
|
|
} |
263
|
|
|
|
} |
264
|
|
|
|
|
265
|
|
|
|
sub getClassifications { |
266
|
|
9741
|
1
|
my ($self,$class) = @_; |
267
|
100
|
|
|
return @{$self->{_class}} if(exists $self->{_class} && defined $self->{_class}); |
268
|
|
|
|
return undef; |
269
|
|
|
|
} |
270
|
|
|
|
|
271
|
|
|
|
sub hasClassification { |
272
|
|
7843
|
1
|
my ($self,$class) = @_; |
273
|
50
|
|
|
if(defined($self->{_class})){ |
274
|
100
|
16135
|
|
if(first {$_ eq $class} @{$self->{_class}}){ |
275
|
|
|
|
return 1; |
276
|
|
|
|
} else { |
277
|
|
|
|
return 0; |
278
|
|
|
|
} |
279
|
|
|
|
} |
280
|
|
|
|
return 0; |
281
|
|
|
|
} |
282
|
|
|
|
|
283
|
|
|
|
|
284
|
|
|
|
__END__ |
285
|
|
|
|
|
286
|
|
|
|
=head1 NAME |
287
|
|
|
|
|
288
|
|
|
|
Sanger::CGP::Vagrent::Data::Annotation - Data object containing the description of an variation |
289
|
|
|
|
within a sequence |
290
|
|
|
|
|
291
|
|
|
|
=head1 DESCRIPTION |
292
|
|
|
|
|
293
|
|
|
|
This holds annotation for a variation against a defined piece of sequence |
294
|
|
|
|
|
295
|
|
|
|
=head1 METHODS |
296
|
|
|
|
|
297
|
|
|
|
=head2 Constructor |
298
|
|
|
|
|
299
|
|
|
|
=head3 new |
300
|
|
|
|
|
301
|
|
|
|
=over |
302
|
|
|
|
|
303
|
|
|
|
=item Usage : |
304
|
|
|
|
|
305
|
|
|
|
my $annot = Sanger::CGP::Vagrent::Data::Annotation->new(%params); |
306
|
|
|
|
|
307
|
|
|
|
=item Function : |
308
|
|
|
|
|
309
|
|
|
|
Builds a new Sanger::CGP::Vagrent::Data::Annotation object |
310
|
|
|
|
|
311
|
|
|
|
=item Returns : |
312
|
|
|
|
|
313
|
|
|
|
L<Sanger::CGP::Vagrent::Data::Annotation|Sanger::CGP::Vagrent::Data::Annotation> object initialized with parameter values |
314
|
|
|
|
|
315
|
|
|
|
=item Params : |
316
|
|
|
|
|
317
|
|
|
|
acc => Accession for the sequence record being annotated against |
318
|
|
|
|
accversion => version of the sequence record |
319
|
|
|
|
db => source DB the sequence record came from |
320
|
|
|
|
dbversion => version of the source DB |
321
|
|
|
|
seqlength => length of sequence in the sequence record |
322
|
|
|
|
context => sequence context of the annotation (defined by context constants) |
323
|
|
|
|
type => variation type the annotation describes (defined by type constants) |
324
|
|
|
|
subtype => variation type the annotation describes (defined by subtype constants) |
325
|
|
|
|
minpos => minimum coordinate in the sequence |
326
|
|
|
|
maxpos => maximum coordinate in the sequence |
327
|
|
|
|
minOffset => offset distance away from the minpos (typically used for splice site mutations) |
328
|
|
|
|
maxOffset => offset distance away from the maxpos (typically used for splice site mutations) |
329
|
|
|
|
wt => wild type sequence of variant |
330
|
|
|
|
mt => mutant sequence of variant |
331
|
|
|
|
description => HGVS style description string |
332
|
|
|
|
|
333
|
|
|
|
=back |
334
|
|
|
|
|
335
|
|
|
|
=head2 Attributes |
336
|
|
|
|
|
337
|
|
|
|
=head3 getMinPos |
338
|
|
|
|
|
339
|
|
|
|
=over |
340
|
|
|
|
|
341
|
|
|
|
=item Usage : |
342
|
|
|
|
|
343
|
|
|
|
my $min = $a->getMinPos; |
344
|
|
|
|
|
345
|
|
|
|
=item Function : |
346
|
|
|
|
|
347
|
|
|
|
Returns the lowest coordinate of the annotation on the sequence |
348
|
|
|
|
|
349
|
|
|
|
=item Returns : |
350
|
|
|
|
|
351
|
|
|
|
Integer |
352
|
|
|
|
|
353
|
|
|
|
=back |
354
|
|
|
|
|
355
|
|
|
|
=head3 getMinOffset |
356
|
|
|
|
|
357
|
|
|
|
=over |
358
|
|
|
|
|
359
|
|
|
|
=item Usage : |
360
|
|
|
|
|
361
|
|
|
|
my $minOff = $a->getMinOffset; |
362
|
|
|
|
|
363
|
|
|
|
=item Function : |
364
|
|
|
|
|
365
|
|
|
|
Returns the offset value from the minimim coordinate |
366
|
|
|
|
|
367
|
|
|
|
=item Returns : |
368
|
|
|
|
|
369
|
|
|
|
Signed integer |
370
|
|
|
|
|
371
|
|
|
|
=back |
372
|
|
|
|
|
373
|
|
|
|
=head3 getMaxPos |
374
|
|
|
|
|
375
|
|
|
|
=over |
376
|
|
|
|
|
377
|
|
|
|
=item Usage : |
378
|
|
|
|
|
379
|
|
|
|
my $min = $a->getMaxPos; |
380
|
|
|
|
|
381
|
|
|
|
=item Function : |
382
|
|
|
|
|
383
|
|
|
|
Returns the highest coordinate of the annotation on the sequence |
384
|
|
|
|
|
385
|
|
|
|
=item Returns : |
386
|
|
|
|
|
387
|
|
|
|
Integer |
388
|
|
|
|
|
389
|
|
|
|
=back |
390
|
|
|
|
|
391
|
|
|
|
=head3 getMaxOffset |
392
|
|
|
|
|
393
|
|
|
|
=over |
394
|
|
|
|
|
395
|
|
|
|
=item Usage : |
396
|
|
|
|
|
397
|
|
|
|
my $maxOff = $a->getMaxOffset; |
398
|
|
|
|
|
399
|
|
|
|
=item Function : |
400
|
|
|
|
|
401
|
|
|
|
Returns the offset value from the maximum coordinate |
402
|
|
|
|
|
403
|
|
|
|
=item Returns : |
404
|
|
|
|
|
405
|
|
|
|
Signed integer |
406
|
|
|
|
|
407
|
|
|
|
=back |
408
|
|
|
|
|
409
|
|
|
|
=head3 getWt |
410
|
|
|
|
|
411
|
|
|
|
=over |
412
|
|
|
|
|
413
|
|
|
|
=item Usage : |
414
|
|
|
|
|
415
|
|
|
|
my $wtSeq = $a->getWt; |
416
|
|
|
|
|
417
|
|
|
|
=item Function : |
418
|
|
|
|
|
419
|
|
|
|
Returns the wildtype sequence string |
420
|
|
|
|
|
421
|
|
|
|
=item Returns : |
422
|
|
|
|
|
423
|
|
|
|
String |
424
|
|
|
|
|
425
|
|
|
|
=back |
426
|
|
|
|
|
427
|
|
|
|
=head3 getMt |
428
|
|
|
|
|
429
|
|
|
|
=over |
430
|
|
|
|
|
431
|
|
|
|
=item Usage : |
432
|
|
|
|
|
433
|
|
|
|
my $mtSeq = $a->getMt; |
434
|
|
|
|
|
435
|
|
|
|
=item Function : |
436
|
|
|
|
|
437
|
|
|
|
Returns the mutant sequence string |
438
|
|
|
|
|
439
|
|
|
|
=item Returns : |
440
|
|
|
|
|
441
|
|
|
|
String |
442
|
|
|
|
|
443
|
|
|
|
=back |
444
|
|
|
|
|
445
|
|
|
|
=head3 getDescription |
446
|
|
|
|
|
447
|
|
|
|
=over |
448
|
|
|
|
|
449
|
|
|
|
=item Usage : |
450
|
|
|
|
|
451
|
|
|
|
my $desc = $a->getDescription; |
452
|
|
|
|
|
453
|
|
|
|
=item Function |
454
|
|
|
|
|
455
|
|
|
|
An HGVS style description string of the annotation |
456
|
|
|
|
|
457
|
|
|
|
=item Returns |
458
|
|
|
|
|
459
|
|
|
|
String |
460
|
|
|
|
|
461
|
|
|
|
=back |
462
|
|
|
|
|
463
|
|
|
|
=head3 getContext |
464
|
|
|
|
|
465
|
|
|
|
=over |
466
|
|
|
|
|
467
|
|
|
|
=item Usage : |
468
|
|
|
|
|
469
|
|
|
|
my $ctx = $a->getContext; |
470
|
|
|
|
|
471
|
|
|
|
=item Function |
472
|
|
|
|
|
473
|
|
|
|
The context of the annotation, as defined by a context constant value |
474
|
|
|
|
|
475
|
|
|
|
=item Returns |
476
|
|
|
|
|
477
|
|
|
|
String |
478
|
|
|
|
|
479
|
|
|
|
=back |
480
|
|
|
|
|
481
|
|
|
|
=head3 getType |
482
|
|
|
|
|
483
|
|
|
|
=over |
484
|
|
|
|
|
485
|
|
|
|
=item Usage : |
486
|
|
|
|
|
487
|
|
|
|
my $type = $a->getType; |
488
|
|
|
|
|
489
|
|
|
|
=item Function |
490
|
|
|
|
|
491
|
|
|
|
The type of the annotation, as defined by a type constant value |
492
|
|
|
|
|
493
|
|
|
|
=item Returns |
494
|
|
|
|
|
495
|
|
|
|
String |
496
|
|
|
|
|
497
|
|
|
|
=back |
498
|
|
|
|
|
499
|
|
|
|
=head3 getSubtype |
500
|
|
|
|
|
501
|
|
|
|
=over |
502
|
|
|
|
|
503
|
|
|
|
=item Usage : |
504
|
|
|
|
|
505
|
|
|
|
my $subtype = $a->getSubtype; |
506
|
|
|
|
|
507
|
|
|
|
=item Function |
508
|
|
|
|
|
509
|
|
|
|
The subtype of the annotation, as defined by a subtype constant value |
510
|
|
|
|
|
511
|
|
|
|
=item Returns |
512
|
|
|
|
|
513
|
|
|
|
String |
514
|
|
|
|
|
515
|
|
|
|
=back |
516
|
|
|
|
|
517
|
|
|
|
=head3 getAccession |
518
|
|
|
|
|
519
|
|
|
|
=over |
520
|
|
|
|
|
521
|
|
|
|
=item Usage : |
522
|
|
|
|
|
523
|
|
|
|
my $accession = $a->getAccession; |
524
|
|
|
|
|
525
|
|
|
|
=item Function |
526
|
|
|
|
|
527
|
|
|
|
The accession of the sequence record the annotation is built against |
528
|
|
|
|
|
529
|
|
|
|
=item Returns |
530
|
|
|
|
|
531
|
|
|
|
String |
532
|
|
|
|
|
533
|
|
|
|
=back |
534
|
|
|
|
|
535
|
|
|
|
=head3 getSequenceVersion |
536
|
|
|
|
|
537
|
|
|
|
=over |
538
|
|
|
|
|
539
|
|
|
|
=item Usage : |
540
|
|
|
|
|
541
|
|
|
|
my $vers = $a->getSequenceVersion; |
542
|
|
|
|
|
543
|
|
|
|
=item Function |
544
|
|
|
|
|
545
|
|
|
|
The version of the sequence record the annotation is built against |
546
|
|
|
|
|
547
|
|
|
|
=item Returns |
548
|
|
|
|
|
549
|
|
|
|
String |
550
|
|
|
|
|
551
|
|
|
|
=back |
552
|
|
|
|
|
553
|
|
|
|
=head3 getDatabase |
554
|
|
|
|
|
555
|
|
|
|
=over |
556
|
|
|
|
|
557
|
|
|
|
=item Usage : |
558
|
|
|
|
|
559
|
|
|
|
my $db = $a->getDatabase; |
560
|
|
|
|
|
561
|
|
|
|
=item Function |
562
|
|
|
|
|
563
|
|
|
|
The database the sequence record originated from |
564
|
|
|
|
|
565
|
|
|
|
=item Returns |
566
|
|
|
|
|
567
|
|
|
|
String |
568
|
|
|
|
|
569
|
|
|
|
=back |
570
|
|
|
|
|
571
|
|
|
|
=head3 getDatabaseVersion |
572
|
|
|
|
|
573
|
|
|
|
=over |
574
|
|
|
|
|
575
|
|
|
|
=item Usage : |
576
|
|
|
|
|
577
|
|
|
|
my $dbVersion = $a->getDatabaseVersion; |
578
|
|
|
|
|
579
|
|
|
|
=item Function |
580
|
|
|
|
|
581
|
|
|
|
The version of the database the sequence record originated from |
582
|
|
|
|
|
583
|
|
|
|
=item Returns |
584
|
|
|
|
|
585
|
|
|
|
String |
586
|
|
|
|
|
587
|
|
|
|
=back |
588
|
|
|
|
|
589
|
|
|
|
=head3 getSequenceLength |
590
|
|
|
|
|
591
|
|
|
|
=over |
592
|
|
|
|
|
593
|
|
|
|
=item Usage : |
594
|
|
|
|
|
595
|
|
|
|
my $seqLength = $a->getSequenceLength; |
596
|
|
|
|
|
597
|
|
|
|
=item Function |
598
|
|
|
|
|
599
|
|
|
|
The full length of the sequence in the sequence record |
600
|
|
|
|
|
601
|
|
|
|
=item Returns |
602
|
|
|
|
|
603
|
|
|
|
Integer |
604
|
|
|
|
|
605
|
|
|
|
=back |
606
|
|
|
|
|
607
|
|
|
|
=head3 addClassification |
608
|
|
|
|
|
609
|
|
|
|
=over |
610
|
|
|
|
|
611
|
|
|
|
=item Usage : |
612
|
|
|
|
|
613
|
|
|
|
$a->addClassification($class1,$class2); |
614
|
|
|
|
|
615
|
|
|
|
=item Function |
616
|
|
|
|
|
617
|
|
|
|
Appends one or more classification terms to the annotation |
618
|
|
|
|
|
619
|
|
|
|
=item Params |
620
|
|
|
|
|
621
|
|
|
|
An array of classification terms (Strings) |
622
|
|
|
|
|
623
|
|
|
|
=item Returns |
624
|
|
|
|
|
625
|
|
|
|
None |
626
|
|
|
|
|
627
|
|
|
|
=back |
628
|
|
|
|
|
629
|
|
|
|
=head3 getClassifications |
630
|
|
|
|
|
631
|
|
|
|
=over |
632
|
|
|
|
|
633
|
|
|
|
=item Usage : |
634
|
|
|
|
|
635
|
|
|
|
my @classes = $a->getClassifications; |
636
|
|
|
|
|
637
|
|
|
|
=item Function |
638
|
|
|
|
|
639
|
|
|
|
Returns the stored classification terms |
640
|
|
|
|
|
641
|
|
|
|
=item Returns |
642
|
|
|
|
|
643
|
|
|
|
Array of Strings, or undef if none |
644
|
|
|
|
|
645
|
|
|
|
=back |
646
|
|
|
|
|
647
|
|
|
|
=head2 Functions |
648
|
|
|
|
|
649
|
|
|
|
=head3 hasClassification |
650
|
|
|
|
|
651
|
|
|
|
=over |
652
|
|
|
|
|
653
|
|
|
|
=item Usage : |
654
|
|
|
|
|
655
|
|
|
|
if($a->hasClassification($checkClass)){ |
656
|
|
|
|
..... |
657
|
|
|
|
} |
658
|
|
|
|
|
659
|
|
|
|
=item Function |
660
|
|
|
|
|
661
|
|
|
|
Checks an annotation to see if it already contains the specified class |
662
|
|
|
|
|
663
|
|
|
|
=item Returns |
664
|
|
|
|
|
665
|
|
|
|
Boolean, 1 or 0 |
666
|
|
|
|
|
667
|
|
|
|
=back |
668
|
|
|
|
|
669
|
|
|
|
=head2 Constants |
670
|
|
|
|
|
671
|
|
|
|
=head3 getmRNAAnnotationContext |
672
|
|
|
|
|
673
|
|
|
|
=over |
674
|
|
|
|
|
675
|
|
|
|
=item Usage : |
676
|
|
|
|
|
677
|
|
|
|
my $ctx = $anno->getmRNAAnnotationContext(); |
678
|
|
|
|
my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext(); |
679
|
|
|
|
|
680
|
|
|
|
=item Function : |
681
|
|
|
|
|
682
|
|
|
|
Constant lookup, returns the mRNA Annotation Context value |
683
|
|
|
|
|
684
|
|
|
|
=item Returns : |
685
|
|
|
|
|
686
|
|
|
|
String |
687
|
|
|
|
|
688
|
|
|
|
=back |
689
|
|
|
|
|
690
|
|
|
|
=head3 getCDSAnnotationContext |
691
|
|
|
|
|
692
|
|
|
|
=over |
693
|
|
|
|
|
694
|
|
|
|
=item Usage : |
695
|
|
|
|
|
696
|
|
|
|
my $ctx = $anno->getCDSAnnotationContext(); |
697
|
|
|
|
my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext(); |
698
|
|
|
|
|
699
|
|
|
|
=item Function : |
700
|
|
|
|
|
701
|
|
|
|
Constant lookup, returns the CDS Annotation Context value |
702
|
|
|
|
|
703
|
|
|
|
=item Returns : |
704
|
|
|
|
|
705
|
|
|
|
String |
706
|
|
|
|
|
707
|
|
|
|
=back |
708
|
|
|
|
|
709
|
|
|
|
=head3 getProteinAnnotationContext |
710
|
|
|
|
|
711
|
|
|
|
=over |
712
|
|
|
|
|
713
|
|
|
|
=item Usage : |
714
|
|
|
|
|
715
|
|
|
|
my $ctx = $anno->getProteinAnnotationContext(); |
716
|
|
|
|
my $ctx = Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext(); |
717
|
|
|
|
|
718
|
|
|
|
=item Function : |
719
|
|
|
|
|
720
|
|
|
|
Constant lookup, returns the Protein Annotation Context value |
721
|
|
|
|
|
722
|
|
|
|
=item Returns : |
723
|
|
|
|
|
724
|
|
|
|
String |
725
|
|
|
|
|
726
|
|
|
|
=back |
727
|
|
|
|
|
728
|
|
|
|
=head3 getSubstitutionAnnotationType |
729
|
|
|
|
|
730
|
|
|
|
=over |
731
|
|
|
|
|
732
|
|
|
|
=item Usage : |
733
|
|
|
|
|
734
|
|
|
|
my $type = $anno->getSubstitutionAnnotationType(); |
735
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getSubstitutionAnnotationType(); |
736
|
|
|
|
|
737
|
|
|
|
=item Function : |
738
|
|
|
|
|
739
|
|
|
|
Constant lookup, returns the Substitution Annotation Type value |
740
|
|
|
|
|
741
|
|
|
|
=item Returns : |
742
|
|
|
|
|
743
|
|
|
|
String |
744
|
|
|
|
|
745
|
|
|
|
=back |
746
|
|
|
|
|
747
|
|
|
|
=head3 getDeletionAnnotationType |
748
|
|
|
|
|
749
|
|
|
|
=over |
750
|
|
|
|
|
751
|
|
|
|
=item Usage : |
752
|
|
|
|
|
753
|
|
|
|
my $type = $anno->getDeletionAnnotationType(); |
754
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getDeletionAnnotationType(); |
755
|
|
|
|
|
756
|
|
|
|
=item Function : |
757
|
|
|
|
|
758
|
|
|
|
Constant lookup, returns the Deletion Annotation Type value |
759
|
|
|
|
|
760
|
|
|
|
=item Returns : |
761
|
|
|
|
|
762
|
|
|
|
String |
763
|
|
|
|
|
764
|
|
|
|
=back |
765
|
|
|
|
|
766
|
|
|
|
=head3 getInsertionAnnotationType |
767
|
|
|
|
|
768
|
|
|
|
=over |
769
|
|
|
|
|
770
|
|
|
|
=item Usage : |
771
|
|
|
|
|
772
|
|
|
|
my $type = $anno->getInsertionAnnotationType(); |
773
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getInsertionAnnotationType(); |
774
|
|
|
|
|
775
|
|
|
|
=item Function : |
776
|
|
|
|
|
777
|
|
|
|
Constant lookup, returns the Insertion Annotation Type value |
778
|
|
|
|
|
779
|
|
|
|
=item Returns : |
780
|
|
|
|
|
781
|
|
|
|
String |
782
|
|
|
|
|
783
|
|
|
|
=back |
784
|
|
|
|
|
785
|
|
|
|
=head3 getComplexAnnotationType |
786
|
|
|
|
|
787
|
|
|
|
=over |
788
|
|
|
|
|
789
|
|
|
|
=item Usage : |
790
|
|
|
|
|
791
|
|
|
|
my $type = $anno->getComplexAnnotationType(); |
792
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getComplexAnnotationType(); |
793
|
|
|
|
|
794
|
|
|
|
=item Function : |
795
|
|
|
|
|
796
|
|
|
|
Constant lookup, returns the Complex Annotation Type value |
797
|
|
|
|
|
798
|
|
|
|
=item Returns : |
799
|
|
|
|
|
800
|
|
|
|
String |
801
|
|
|
|
|
802
|
|
|
|
=back |
803
|
|
|
|
|
804
|
|
|
|
=head3 getFrameShiftAnnotationType |
805
|
|
|
|
|
806
|
|
|
|
=over |
807
|
|
|
|
|
808
|
|
|
|
=item Usage : |
809
|
|
|
|
|
810
|
|
|
|
my $type = $anno->getFrameShiftAnnotationType(); |
811
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getFrameShiftAnnotationType(); |
812
|
|
|
|
|
813
|
|
|
|
=item Function : |
814
|
|
|
|
|
815
|
|
|
|
Constant lookup, returns the Frameshift Annotation Type value |
816
|
|
|
|
|
817
|
|
|
|
=item Returns : |
818
|
|
|
|
|
819
|
|
|
|
String |
820
|
|
|
|
|
821
|
|
|
|
=back |
822
|
|
|
|
|
823
|
|
|
|
=head3 getUnknownAnnotationType |
824
|
|
|
|
|
825
|
|
|
|
=over |
826
|
|
|
|
|
827
|
|
|
|
=item Usage : |
828
|
|
|
|
|
829
|
|
|
|
my $type = $anno->getUnknownAnnotationType(); |
830
|
|
|
|
my $type = Sanger::CGP::Vagrent::Data::Annotation::getUnknownAnnotationType(); |
831
|
|
|
|
|
832
|
|
|
|
=item Function : |
833
|
|
|
|
|
834
|
|
|
|
Constant lookup, returns the Unknown Annotation Type value |
835
|
|
|
|
|
836
|
|
|
|
=item Returns : |
837
|
|
|
|
|
838
|
|
|
|
String |
839
|
|
|
|
|
840
|
|
|
|
=back |
841
|
|
|
|
|
842
|
|
|
|
=head3 getPositionKnownSubtype |
843
|
|
|
|
|
844
|
|
|
|
=over |
845
|
|
|
|
|
846
|
|
|
|
=item Usage : |
847
|
|
|
|
|
848
|
|
|
|
my $subtype = $anno->getPositionKnownSubtype(); |
849
|
|
|
|
my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionKnownSubtype(); |
850
|
|
|
|
|
851
|
|
|
|
=item Function : |
852
|
|
|
|
|
853
|
|
|
|
Constant lookup, returns the Position Known Subtype value |
854
|
|
|
|
|
855
|
|
|
|
=item Returns : |
856
|
|
|
|
|
857
|
|
|
|
String |
858
|
|
|
|
|
859
|
|
|
|
=back |
860
|
|
|
|
|
861
|
|
|
|
=head3 getPositionOffsetSubtype |
862
|
|
|
|
|
863
|
|
|
|
=over |
864
|
|
|
|
|
865
|
|
|
|
=item Usage : |
866
|
|
|
|
|
867
|
|
|
|
my $subtype = $anno->getPositionOffsetSubtype(); |
868
|
|
|
|
my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffsetSubtype(); |
869
|
|
|
|
|
870
|
|
|
|
=item Function : |
871
|
|
|
|
|
872
|
|
|
|
Constant lookup, returns the Position Offset Subtype value |
873
|
|
|
|
|
874
|
|
|
|
=item Returns : |
875
|
|
|
|
|
876
|
|
|
|
String |
877
|
|
|
|
|
878
|
|
|
|
=back |
879
|
|
|
|
|
880
|
|
|
|
=head3 getPositionOffSequenceSubtype |
881
|
|
|
|
|
882
|
|
|
|
=over |
883
|
|
|
|
|
884
|
|
|
|
=item Usage : |
885
|
|
|
|
|
886
|
|
|
|
my $subtype = $anno->getPositionOffSequenceSubtype(); |
887
|
|
|
|
my $subtype = Sanger::CGP::Vagrent::Data::Annotation::getPositionOffSequenceSubtype(); |
888
|
|
|
|
|
889
|
|
|
|
=item Function : |
890
|
|
|
|
|
891
|
|
|
|
Constant lookup, returns the Position Off-Sequence Subtype value |
892
|
|
|
|
|
893
|
|
|
|
=item Returns : |
894
|
|
|
|
|
895
|
|
|
|
String |
896
|
|
|
|
|
897
|
|
|
|
=back |
898
|
|
|
|
|
899
|
|
|
|
|