comparison variant_effect_predictor/Bio/EnsEMBL/OperonTranscript.pm @ 0:1f6dce3d34e0

Uploaded
author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1f6dce3d34e0
1
2 =head1 LICENSE
3
4 Copyright (c) 1999-2012 The European Bioinformatics Institute and
5 Genome Research Limited. All rights reserved.
6
7 This software is distributed under a modified Apache license.
8 For license details, please see
9
10 http://www.ensembl.org/info/about/code_licence.html
11
12 =head1 CONTACT
13
14 Please email comments or questions to the public Ensembl
15 developers list at <dev@ensembl.org>.
16
17 Questions may also be sent to the Ensembl help desk at
18 <helpdesk@ensembl.org>.
19
20 =cut
21
22 =head1 NAME
23
24 Bio::EnsEMBL::OperonTranscript - Object representing a polycistronic transcript that is part of an operon
25
26 =head1 SYNOPSIS
27
28 my $operon_transcript =
29 Bio::EnsEMBL::OperonTranscript->new( -START => $start,
30 -END => $end,
31 -STRAND => $strand,
32 -SLICE => $slice );
33 $operon->add_OperonTranscript($operon_transcript);
34
35 =head1 DESCRIPTION
36
37 A representation of a polycistronic transcript from an operon within the Ensembl system. An operon is a collection of one or more polycistronic transcripts, which contain one or more genes.
38
39 =head1 METHODS
40
41 =cut
42
43 package Bio::EnsEMBL::OperonTranscript;
44
45 use strict;
46 use warnings;
47
48 use Bio::EnsEMBL::Feature;
49 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
50 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
51 use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
52
53 use vars qw(@ISA);
54 @ISA = qw(Bio::EnsEMBL::Feature);
55
56 =head2 new
57
58 Arg [-START] :
59 int - start postion of the operon transcript
60 Arg [-END] :
61 int - end position of the operon transcript
62 Arg [-STRAND] :
63 int - 1,-1 tehe strand the operon transcript is on
64 Arg [-SLICE] :
65 Bio::EnsEMBL::Slice - the slice the operon transcript is on
66 Arg [-STABLE_ID] :
67 string - the stable identifier of this operon transcript
68 Arg [-VERSION] :
69 int - the version of the stable identifier of this operon transcript
70 Arg [-CREATED_DATE]:
71 string - the date the operon transcript was created
72 Arg [-MODIFIED_DATE]:
73 string - the date the operon transcript was last modified
74
75 Example : $gene = Bio::EnsEMBL::OperonTranscript->new(...);
76 Description: Creates a new operon transcript object
77 Returntype : Bio::EnsEMBL::OperonTranscript
78 Exceptions : none
79 Caller : general
80 Status : Stable
81
82 =cut
83
84 sub new {
85 my $caller = shift;
86
87 my $class = ref($caller) || $caller;
88 my $self = $class->SUPER::new(@_);
89 my ( $stable_id, $version, $created_date, $modified_date, $display_label ) =
90 rearrange( [ 'STABLE_ID', 'VERSION',
91 'CREATED_DATE', 'MODIFIED_DATE', 'DISPLAY_LABEL' ],
92 @_ );
93
94 $self->stable_id($stable_id);
95 $self->version($version);
96 $self->{'created_date'} = $created_date;
97 $self->{'modified_date'} = $modified_date;
98 $self->display_label($display_label);
99 return $self;
100 }
101
102 =head2 created_date
103
104 Arg [1] : (optional) String - created date to set (as a UNIX time int)
105 Example : $gene->created_date('1141948800');
106 Description: Getter/setter for attribute created_date
107 Returntype : String
108 Exceptions : none
109 Caller : general
110 Status : Stable
111
112 =cut
113
114 sub created_date {
115 my $self = shift;
116 $self->{'created_date'} = shift if ( @_ );
117 return $self->{'created_date'};
118 }
119
120
121 =head2 modified_date
122
123 Arg [1] : (optional) String - modified date to set (as a UNIX time int)
124 Example : $gene->modified_date('1141948800');
125 Description: Getter/setter for attribute modified_date
126 Returntype : String
127 Exceptions : none
128 Caller : general
129 Status : Stable
130
131 =cut
132
133 sub modified_date {
134 my $self = shift;
135 $self->{'modified_date'} = shift if ( @_ );
136 return $self->{'modified_date'};
137 }
138
139
140 =head2 display_label
141
142 Arg [1] : (optional) String - the name/label to set
143 Example : $operon->name('accBCD');
144 Description: Getter/setter for attribute name.
145 Returntype : String or undef
146 Exceptions : none
147 Caller : general
148 Status : Stable
149
150 =cut
151
152 sub display_label {
153 my $self = shift;
154 $self->{'display_label'} = shift if (@_);
155 return $self->{'display_label'};
156 }
157
158 =head2 stable_id
159
160 Arg [1] : (optional) String - the stable ID to set
161 Example : $operon->stable_id("accR2A");
162 Description: Getter/setter for stable id for this operon transcript.
163 Returntype : String
164 Exceptions : none
165 Caller : general
166 Status : Stable
167
168 =cut
169
170 sub stable_id {
171 my $self = shift;
172 $self->{'stable_id'} = shift if (@_);
173 return $self->{'stable_id'};
174 }
175
176 =head2 version
177
178 Arg [1] : (optional) Int - the stable ID version to set
179 Example : $operon->version(1);
180 Description: Getter/setter for stable id version for this operon transcript.
181 Returntype : Int
182 Exceptions : none
183 Caller : general
184 Status : Stable
185
186 =cut
187 sub version {
188 my $self = shift;
189 $self->{'version'} = shift if(@_);
190 return $self->{'version'};
191 }
192
193 =head2 operon
194
195 Example : $operon = $ot->operon();
196 Description: getter for the operon to which this transcript belongs
197 Returntype : Bio::EnsEMBL::Operon
198 Exceptions : none
199 Caller : general
200 Status : Stable
201
202 =cut
203 sub operon {
204 my $self = shift;
205 if ( !exists $self->{'operon'} ) {
206 if ( defined $self->adaptor() ) {
207 my $ta = $self->adaptor()->db()->get_OperonAdaptor();
208 my $operon = $ta->fetch_by_operon_transcript($self);
209 $self->{'operon'} = $operon;
210 }
211 }
212 return $self->{'operon'};
213 }
214
215 =head2 get_all_Genes
216
217 Example : $genes = $ot->get_all_Genes();
218 Description: get all the genes that are attached to this operon transcript
219 Returntype : Arrayref of Bio::EnsEMBL::Gene
220 Exceptions : none
221 Caller : general
222 Status : Stable
223
224 =cut
225 sub get_all_Genes {
226 my $self = shift;
227 if(! defined $self->{_gene_array}) {
228 if(defined $self->dbID() && defined $self->adaptor()) {
229 my $ta = $self->adaptor()->db()->get_OperonTranscriptAdaptor();
230 my $transcripts = $ta->fetch_genes_by_operon_transcript($self);
231 $self->{_gene_array} = $transcripts;
232 }
233 else {
234 $self->{_gene_array} = [];
235 }
236 }
237 return $self->{_gene_array};
238 }
239 =head2 add_gene
240
241 Arg [1] : Bio::EnsEMBL::Gene - gene to attach to this polycistronic transcript
242 Example : $operon->add_gene($gene);
243 Description: Attach a gene to this polycistronic transcript
244 Exceptions : if argument is not Bio::EnsEMBL::Gene
245 Caller : general
246 Status : Stable
247
248 =cut
249 sub add_gene {
250 my ($self,$gene) = @_;
251 assert_ref($gene,'Bio::EnsEMBL::Gene');
252 push @{$self->get_all_Genes()},$gene;
253 return;
254 }
255
256 =head2 add_DBEntry
257
258 Arg [1] : Bio::EnsEMBL::DBEntry $dbe
259 The dbEntry to be added
260 Example : my $dbe = Bio::EnsEMBL::DBEntery->new(...);
261 $operon->add_DBEntry($dbe);
262 Description: Associates a DBEntry with this operon. Note that adding DBEntries
263 will prevent future lazy-loading of DBEntries for this operon
264 (see get_all_DBEntries).
265 Returntype : none
266 Exceptions : thrown on incorrect argument type
267 Caller : general
268 Status : Stable
269
270 =cut
271
272 sub add_DBEntry {
273 my $self = shift;
274 my $dbe = shift;
275
276 unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
277 throw('Expected DBEntry argument');
278 }
279
280 $self->{'dbentries'} ||= [];
281 push @{$self->{'dbentries'}}, $dbe;
282 }
283
284
285 =head2 get_all_Attributes
286
287 Arg [1] : (optional) String $attrib_code
288 The code of the attribute type to retrieve values for
289 Example : my ($author) = @{ $ot->get_all_Attributes('author') };
290 my @ot_attributes = @{ $ot->get_all_Attributes };
291 Description: Gets a list of Attributes of this operon transcript.
292 Optionally just get Attributes for given code.
293 Returntype : Listref of Bio::EnsEMBL::Attribute
294 Exceptions : warning if gene does not have attached adaptor and attempts lazy
295 load.
296 Caller : general
297 Status : Stable
298
299 =cut
300
301 sub get_all_Attributes {
302 my $self = shift;
303 my $attrib_code = shift;
304
305 if ( !exists $self->{'attributes'} ) {
306 if ( !$self->adaptor() ) {
307 return [];
308 }
309
310 my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
311 $self->{'attributes'} = $attribute_adaptor->fetch_all_by_OperonTranscript($self);
312 }
313
314 if ( defined $attrib_code ) {
315 my @results =
316 grep { uc( $_->code() ) eq uc($attrib_code) }
317 @{ $self->{'attributes'} };
318 return \@results;
319 } else {
320 return $self->{'attributes'};
321 }
322 }
323
324 =head2 get_all_DBEntries
325
326 Arg [1] : (optional) String, external database name
327
328 Arg [2] : (optional) String, external_db type
329
330 Example : @dbentries = @{ $gene->get_all_DBEntries() };
331
332 Description: Retrieves DBEntries (xrefs) for this operon transcript. This does
333 *not* include DBEntries that are associated with the
334 transcripts and corresponding translations of this
335 gene (see get_all_DBLinks()).
336
337 This method will attempt to lazy-load DBEntries
338 from a database if an adaptor is available and no
339 DBEntries are present on the gene (i.e. they have not
340 already been added or loaded).
341
342 Return type: Listref of Bio::EnsEMBL::DBEntry objects
343 Exceptions : none
344 Caller : get_all_DBLinks, OperontTranscriptAdaptor::store
345 Status : Stable
346
347 =cut
348
349 sub get_all_DBEntries {
350 my ( $self, $db_name_exp, $ex_db_type ) = @_;
351
352 my $cache_name = 'dbentries';
353
354 if ( defined($db_name_exp) ) {
355 $cache_name .= $db_name_exp;
356 }
357
358 if ( defined($ex_db_type) ) {
359 $cache_name .= $ex_db_type;
360 }
361
362 # if not cached, retrieve all of the xrefs for this gene
363 if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) ) {
364 $self->{$cache_name} =
365 $self->adaptor()->db()->get_DBEntryAdaptor()
366 ->fetch_all_by_Operon( $self->operon(), $db_name_exp, $ex_db_type );
367 }
368
369 $self->{$cache_name} ||= [];
370
371 return $self->{$cache_name};
372 }
373
374 1;
375