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

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date Thu, 11 Apr 2013 02:01:53 -0400
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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::DBSQL::SlicingEventAdaptor - Database adaptor for the retrieval and
24 storage of SplicingEvent objects
25
26 =head1 SYNOPSIS
27
28 use Bio::EnsEMBL::Registry;
29
30 Bio::EnsEMBL::Registry->load_registry_from_db(
31 -host => 'ensembldb.ensembl.org',
32 -user => 'anonymous',
33 );
34
35 $se_adaptor =
36 Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEvent" );
37
38 $se = $se_adaptor->fetch_by_dbID(12);
39
40 $slice_adaptor =
41 Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
42
43 $slice =
44 $slice_adaptor->fetch_by_region( 'chromosome', '1', 1, 1000000 );
45
46 @ase = @{ $se_adaptor->fetch_all_by_Slice($slice) };
47
48 =head1 DESCRIPTION
49
50 This is a database aware adaptor for the retrieval and storage ofSlicingEvents
51 objects.
52
53 =head1 METHODS
54
55 =cut
56 package Bio::EnsEMBL::DBSQL::SplicingEventAdaptor;
57
58 use strict;
59
60 use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
61 use Bio::EnsEMBL::DBSQL::SliceAdaptor;
62 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
63 use Bio::EnsEMBL::DBSQL::DBAdaptor;
64 use Bio::EnsEMBL::SplicingEvent;
65
66 use vars '@ISA';
67 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
68
69
70 =head2 list_dbIDs
71
72 Example : @gene_ids = @{$gene_adaptor->list_dbIDs()};
73 Description: Gets an array of internal ids for all genes in the current db
74 Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
75 Returntype : Listref of Ints
76 Exceptions : none
77 Caller : general
78 Status : Stable
79
80 =cut
81
82 sub list_dbIDs {
83 my ($self,$ordered) = @_;
84
85 return $self->_list_dbIDs("splicing_event", undef, $ordered);
86 }
87
88
89 =head2 fetch_all_by_Slice
90
91 Arg [1] : Bio::EnsEMBL::Slice $slice
92 The slice to fetch genes on.
93 Arg [2] : type of Transcript event
94 Arg [3] : (optional) boolean $load_features
95 If true, transcript will be loaded immediately rather
96 than lazy loaded later.
97 =cut
98
99 sub fetch_all_by_Slice {
100 my ( $self, $slice, $type, $load_features ) = @_;
101
102 my $constraint = '';
103
104 if ( defined($type) ) {
105 $constraint .= sprintf( " AND at.code = %s",
106 $self->dbc()->db_handle()->quote($type) );
107 }
108
109 my $tes =
110 $self->SUPER::fetch_all_by_Slice_constraint( $slice, $constraint );
111
112 # Is there any use in having a splice event without the pairs and
113 # features??
114
115 if ( !$load_features || scalar( @{$tes} ) < 2 ) {
116 return $tes;
117 }
118
119 # Load pairs and features.
120 foreach my $te ( @{$tes} ) {
121 $te->get_all_Features();
122 $te->get_all_Pairs();
123 }
124
125 return $tes;
126 } ## end sub fetch_all_by_Slice
127
128
129 sub fetch_all_by_Gene {
130 my ( $self, $gene ) = @_;
131
132 my $sth = $self->dbc->prepare(
133 q(
134 SELECT se.splicing_event_id,
135 se.seq_region_id,
136 se.seq_region_start,
137 se.seq_region_end,
138 se.seq_region_strand,
139 se.name,
140 at.code
141 FROM splicing_event se
142 JOIN attrib_type at USING (attrib_type_id)
143 WHERE se.gene_id =) . $gene->dbID() );
144
145 $sth->execute();
146
147 my ( $splicing_event_id, $seq_region_id, $seq_region_start,
148 $seq_region_end, $seq_region_strand, $name, $type );
149
150 $sth->bind_columns(
151 \( $splicing_event_id, $seq_region_id, $seq_region_start,
152 $seq_region_end, $seq_region_strand, $name,
153 $type ) );
154
155 my @splicing_events;
156
157 my $sa = $self->db()->get_SliceAdaptor();
158
159 while ( $sth->fetch() ) {
160 my $slice =
161 $sa->fetch_by_seq_region_id( $seq_region_id,
162 $seq_region_start,
163 $seq_region_end,
164 $seq_region_strand );
165
166 push( @splicing_events,
167 $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
168 'start' => $seq_region_start,
169 'end' => $seq_region_end,
170 'strand' => $seq_region_strand,
171 'adaptor' => $self,
172 'slice' => $slice,
173 'dbID' => $splicing_event_id,
174 'name' => $name,
175 'gene_id' => $gene->dbID(),
176 'type' => $type } ) );
177 }
178
179 foreach my $te (@splicing_events) {
180 $te->get_all_Features();
181 $te->get_all_Pairs();
182 }
183
184 return \@splicing_events;
185 } ## end sub fetch_all_by_Gene
186
187 sub fetch_all_by_Exon {
188 my ( $self, $exon ) = @_;
189
190 my $sth = $self->dbc()->prepare(
191 q(
192 SELECT DISTINCT splicing_event_id
193 FROM splicing_event_feature
194 WHERE exon_id =) . $exon->dbID() );
195
196 $sth->execute();
197
198 my $se_id;
199 $sth->bind_col( 1, \$se_id );
200
201 my @list;
202 while ( $sth->fetch() ) {
203 push( @list, $se_id );
204 }
205
206 $sth = $self->dbc->prepare(
207 q(
208 SELECT se.splicing_event_id,
209 se.seq_region_id,
210 se.seq_region_start,
211 se.seq_region_end,
212 se.seq_region_strand,
213 se.name,
214 at.code,
215 se.gene_id
216 FROM splicing_event se
217 JOIN attrib_type at USING (attrib_type_id)
218 WHERE se.splicing_event_id in ) . '(' . join( ',', @list ) . ')' );
219
220 $sth->execute();
221
222 my ( $splicing_event_id, $seq_region_id, $seq_region_start,
223 $seq_region_end, $seq_region_strand, $name, $type, $gene_id );
224
225 $sth->bind_columns(
226 \( $splicing_event_id, $seq_region_id, $seq_region_start,
227 $seq_region_end, $seq_region_strand, $name,
228 $type, $gene_id ) );
229
230 my @splicing_events;
231
232 my $sa = $self->db->get_SliceAdaptor();
233
234 while ( $sth->fetch ) {
235 my $slice =
236 $sa->fetch_by_seq_region_id( $seq_region_id,
237 $seq_region_start,
238 $seq_region_end,
239 $seq_region_strand );
240
241 push( @splicing_events,
242 $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
243 'start' => $seq_region_start,
244 'end' => $seq_region_end,
245 'strand' => $seq_region_strand,
246 'adaptor' => $self,
247 'slice' => $slice,
248 'dbID' => $splicing_event_id,
249 'name' => $name,
250 'gene_id' => $gene_id,
251 'type' => $type } ) );
252 }
253
254 foreach my $te (@splicing_events) {
255 $te->get_all_Features();
256 $te->get_all_Pairs();
257 }
258
259 return \@splicing_events;
260 } ## end sub fetch_all_by_Exon
261
262 sub fetch_all_by_Transcript {
263 my ( $self, $transcript ) = @_;
264
265 my $sth = $self->dbc->prepare(
266 q(
267 SELECT DISTINCT splicing_event_id
268 FROM splicing_event_feature
269 WHERE transcript_id =) . $transcript->dbID() );
270
271 $sth->execute();
272
273 my $se_id;
274 $sth->bind_col( 1, \$se_id );
275
276 my @list;
277 while ( $sth->fetch() ) {
278 push( @list, $se_id );
279 }
280
281 $sth = $self->dbc->prepare(
282 q(
283 SELECT se.splicing_event_id,
284 se.seq_region_id,
285 se.seq_region_start,
286 se.seq_region_end,
287 se.seq_region_strand,
288 se.name,
289 at.code,
290 se.gene_id
291 FROM splicing_event se
292 JOIN attrib_type at USING (attrib_type_id)
293 WHERE se.splicing_event_id in ) . '(' . join( ',', @list ) . ')' );
294
295 $sth->execute();
296
297 my ( $splicing_event_id, $seq_region_id, $seq_region_start,
298 $seq_region_end, $seq_region_strand, $name, $type, $gene_id );
299
300 $sth->bind_columns(
301 \( $splicing_event_id, $seq_region_id, $seq_region_start,
302 $seq_region_end, $seq_region_strand, $name,
303 $type, $gene_id ) );
304
305 my @splicing_events;
306
307 my $sa = $self->db()->get_SliceAdaptor();
308
309 while ( $sth->fetch() ) {
310 my $slice =
311 $sa->fetch_by_seq_region_id( $seq_region_id,
312 $seq_region_start,
313 $seq_region_end,
314 $seq_region_strand );
315
316 push( @splicing_events,
317 $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
318 'start' => $seq_region_start,
319 'end' => $seq_region_end,
320 'strand' => $seq_region_strand,
321 'adaptor' => $self,
322 'slice' => $slice,
323 'dbID' => $splicing_event_id,
324 'name' => $name,
325 'gene_id' => $gene_id,
326 'type' => $type } ) );
327 }
328
329 foreach my $te (@splicing_events) {
330 $te->get_all_Features();
331 $te->get_all_Pairs();
332 }
333
334 return \@splicing_events;
335 } ## end sub fetch_all_by_Transcript
336
337 # _tables
338 # Arg [1] : none
339 # Description: PROTECTED implementation of superclass abstract method.
340 # Returns the names, aliases of the tables to use for queries.
341 # Returntype : list of listrefs of strings
342 # Exceptions : none
343 # Caller : internal
344 # Status : At Risk
345
346 sub _tables {
347 return ( [ 'splicing_event', 'se' ], [ 'attrib_type', 'at' ] );
348 }
349
350 # _columns
351 # Arg [1] : none
352 # Example : none
353 # Description: PROTECTED implementation of superclass abstract method.
354 # Returns a list of columns to use for queries.
355 # Returntype : list of strings
356 # Exceptions : none
357 # Caller : internal
358 # Status : At Risk
359
360 sub _columns {
361 return ( 'se.splicing_event_id', 'se.seq_region_id',
362 'se.seq_region_start', 'se.seq_region_end',
363 'se.seq_region_strand', 'se.name',
364 'se.gene_id', 'at.code' );
365 }
366
367 sub _left_join {
368 return ( [ 'attrib_type', 'at.attrib_type_id = se.attrib_type_id' ] );
369 }
370
371 sub _objs_from_sth {
372 my ( $self, $sth, $mapper, $dest_slice ) = @_;
373
374 my ( $splicing_event_id, $seq_region_id, $seq_region_start,
375 $seq_region_end, $seq_region_strand, $name, $gene_id, $type );
376
377 $sth->bind_columns(
378 \( $splicing_event_id, $seq_region_id, $seq_region_start,
379 $seq_region_end, $seq_region_strand, $name,
380 $gene_id, $type ) );
381
382 my $sa = $self->db()->get_SliceAdaptor();
383
384 my @splicing_events;
385 my %slice_hash;
386 my %sr_name_hash;
387 my %sr_cs_hash;
388
389 my $asm_cs;
390 my $cmp_cs;
391 my $asm_cs_vers;
392 my $asm_cs_name;
393 my $cmp_cs_vers;
394 my $cmp_cs_name;
395
396 if ( defined($mapper) ) {
397 $asm_cs = $mapper->assembled_CoordSystem();
398 $cmp_cs = $mapper->component_CoordSystem();
399 $asm_cs_name = $asm_cs->name();
400 $asm_cs_vers = $asm_cs->version();
401 $cmp_cs_name = $cmp_cs->name();
402 $cmp_cs_vers = $cmp_cs->version();
403 }
404
405 my $dest_slice_start;
406 my $dest_slice_end;
407 my $dest_slice_strand;
408 my $dest_slice_length;
409 my $dest_slice_cs;
410 my $dest_slice_sr_name;
411 my $dest_slice_sr_id;
412 my $asma;
413
414 if ( defined($dest_slice) ) {
415 $dest_slice_start = $dest_slice->start();
416 $dest_slice_end = $dest_slice->end();
417 $dest_slice_strand = $dest_slice->strand();
418 $dest_slice_length = $dest_slice->length();
419 $dest_slice_cs = $dest_slice->coord_system();
420 $dest_slice_sr_name = $dest_slice->seq_region_name();
421 $dest_slice_sr_id = $dest_slice->get_seq_region_id();
422 $asma = $self->db->get_AssemblyMapperAdaptor();
423 }
424
425 FEATURE:
426 while ( $sth->fetch() ) {
427 # Need to get the internal_seq_region, if present.
428 $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
429
430 my $slice = $slice_hash{ "ID:" . $seq_region_id };
431 my $dest_mapper = $mapper;
432
433 if ( !$slice ) {
434 $slice = $sa->fetch_by_seq_region_id($seq_region_id);
435 $slice_hash{ "ID:" . $seq_region_id } = $slice;
436 $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
437 $sr_cs_hash{$seq_region_id} = $slice->coord_system();
438 }
439
440 # Obtain a mapper if none was defined, but a dest_seq_region was.
441 if ( !defined($dest_mapper)
442 && defined($dest_slice)
443 && !$dest_slice_cs->equals( $slice->coord_system ) )
444 {
445 $dest_mapper =
446 $asma->fetch_by_CoordSystems( $dest_slice_cs,
447 $slice->coord_system );
448 $asm_cs = $dest_mapper->assembled_CoordSystem();
449 $cmp_cs = $dest_mapper->component_CoordSystem();
450 $asm_cs_name = $asm_cs->name();
451 $asm_cs_vers = $asm_cs->version();
452 $cmp_cs_name = $cmp_cs->name();
453 $cmp_cs_vers = $cmp_cs->version();
454 }
455
456 my $sr_name = $sr_name_hash{$seq_region_id};
457 my $sr_cs = $sr_cs_hash{$seq_region_id};
458
459 # Remap the feature coordinates to another coord system if a mapper
460 # was provided.
461 if ( defined($dest_mapper) ) {
462
463 if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
464 ( $seq_region_id, $seq_region_start,
465 $seq_region_end, $seq_region_strand )
466 =
467 $dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
468 $seq_region_strand, $sr_cs, 1, $dest_slice);
469
470 } else {
471
472 ( $seq_region_id, $seq_region_start,
473 $seq_region_end, $seq_region_strand )
474 = $dest_mapper->fastmap( $sr_name, $seq_region_start,
475 $seq_region_end, $seq_region_strand,
476 $sr_cs );
477 }
478
479 # Skip features that map to gaps or coord system boundaries.
480 if ( !defined($seq_region_id) ) { next FEATURE }
481
482 # Get a slice in the coord system we just mapped to.
483 $slice = $slice_hash{ "ID:" . $seq_region_id } ||=
484 $sa->fetch_by_seq_region_id($seq_region_id);
485 }
486
487 # If a destination slice was provided convert the coords. If the
488 # dest_slice starts at 1 and is foward strand, nothing needs doing.
489 if ( defined($dest_slice) ) {
490 if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) {
491 if ( $dest_slice_strand == 1 ) {
492 $seq_region_start = $seq_region_start - $dest_slice_start + 1;
493 $seq_region_end = $seq_region_end - $dest_slice_start + 1;
494 } else {
495 my $tmp_seq_region_start = $seq_region_start;
496 $seq_region_start = $dest_slice_end - $seq_region_end + 1;
497 $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
498 $seq_region_strand = -$seq_region_strand;
499 }
500 }
501
502 # Throw away features off the end of the requested slice.
503 if ( $seq_region_end < 1
504 || $seq_region_start > $dest_slice_length
505 || ( $dest_slice_sr_id != $seq_region_id ) )
506 {
507 next FEATURE;
508 }
509
510 $slice = $dest_slice;
511 }
512
513 # Finally, create the new splicing_event.
514 push( @splicing_events,
515 $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEvent', {
516 'start' => $seq_region_start,
517 'end' => $seq_region_end,
518 'strand' => $seq_region_strand,
519 'adaptor' => $self,
520 'slice' => $slice,
521 'dbID' => $splicing_event_id,
522 'name' => $name,
523 'gene_id' => $gene_id,
524 'type' => $type } ) );
525
526 } ## end while ( $sth->fetch() )
527
528 return \@splicing_events;
529 } ## end sub _objs_from_sth
530
531
532 1;