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

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author mahtabm
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::PredictionExonAdaptor - Performs database interaction for
24 PredictionExons.
25
26 =head1 SYNOPSIS
27
28 $pea = $database_adaptor->get_PredictionExonAdaptor();
29 $pexon = $pea->fetch_by_dbID();
30
31 my $slice =
32 $database_adaptor->get_SliceAdaptor->fetch_by_region( 'X', 1, 1e6 );
33
34 my @pexons = @{ $pea->fetch_all_by_Slice($slice) };
35
36 =head1 METHODS
37
38 =cut
39
40 package Bio::EnsEMBL::DBSQL::PredictionExonAdaptor;
41
42 use vars qw( @ISA );
43 use strict;
44
45
46 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
47 use Bio::EnsEMBL::PredictionExon;
48 use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
49
50
51 @ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
52
53
54 #_tables
55 #
56 # Arg [1] : none
57 # Example : none
58 # Description: PROTECTED implementation of superclass abstract method
59 # returns the names, aliases of the tables to use for queries
60 # Returntype : list of listrefs of strings
61 # Exceptions : none
62 # Caller : internal
63 #
64
65 sub _tables {
66 return ([ 'prediction_exon', 'pe' ] );
67 }
68
69
70
71 #_columns
72 #
73 # Arg [1] : none
74 # Example : none
75 # Description: PROTECTED implementation of superclass abstract method
76 # returns a list of columns to use for queries
77 # Returntype : list of strings
78 # Exceptions : none
79 # Caller : internal
80
81 sub _columns {
82 my $self = shift;
83
84 return qw( pe.prediction_exon_id
85 pe.seq_region_id
86 pe.seq_region_start
87 pe.seq_region_end
88 pe.seq_region_strand
89 pe.start_phase
90 pe.score
91 pe.p_value );
92 }
93
94
95 # _final_clause
96 #
97 # Arg [1] : none
98 # Example : none
99 # Description: PROTECTED implementation of superclass abstract method
100 # returns a default end for the SQL-query (ORDER BY)
101 # Returntype : string
102 # Exceptions : none
103 # Caller : internal
104
105 sub _final_clause {
106 return "ORDER BY pe.prediction_transcript_id, pe.exon_rank";
107 }
108
109
110 =head2 fetch_all_by_PredictionTranscript
111
112 Arg [1] : Bio::EnsEMBL::PredcitionTranscript $transcript
113 Example : none
114 Description: Retrieves all Exons for the Transcript in 5-3 order
115 Returntype : listref Bio::EnsEMBL::Exon on Transcript slice
116 Exceptions : throws if transcript does not have a slice
117 Caller : Transcript->get_all_Exons()
118 Status : Stable
119
120 =cut
121
122 sub fetch_all_by_PredictionTranscript {
123 my ( $self, $transcript ) = @_;
124 my $constraint = "pe.prediction_transcript_id = ".$transcript->dbID();
125
126 # use 'keep_all' option to keep exons that are off end of slice
127
128 my $tslice = $transcript->slice();
129 my $slice;
130
131 if(!$tslice) {
132 throw("Transcript must have attached slice to retrieve exons.");
133 }
134
135 # use a small slice the same size as the prediction transcript
136 $slice = $self->db->get_SliceAdaptor->fetch_by_Feature($transcript);
137
138 my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint);
139
140 # remap exon coordinates if necessary
141 if($slice->name() ne $tslice->name()) {
142 my @out;
143 foreach my $ex (@$exons) {
144 push @out, $ex->transfer($tslice);
145 }
146 $exons = \@out;
147 }
148
149 return $exons;
150 }
151
152
153
154 =head2 store
155
156 Arg [1] : Bio::EnsEMBL::PredictionExon $exon
157 The exon to store in this database
158 Arg [2] : int $prediction_transcript_id
159 The internal identifier of the prediction exon that that this
160 exon is associated with.
161 Arg [3] : int $rank
162 The rank of the exon in the transcript (starting at 1)
163 Example : $pexon_adaptor->store($pexon, 1211, 2);
164 Description: Stores a PredictionExon in the database
165 Returntype : none
166 Exceptions : thrown if exon does not have a slice attached
167 or if $exon->start, $exon->end, $exon->strand, or $exon->phase
168 are not defined or if $exon is not a Bio::EnsEMBL::PredictionExon
169 Caller : general
170 Status : Stable
171
172 =cut
173
174 sub store {
175 my ( $self, $pexon, $pt_id, $rank ) = @_;
176
177 if(!ref($pexon) || !$pexon->isa('Bio::EnsEMBL::PredictionExon') ) {
178 throw("Expected PredictionExon argument");
179 }
180
181 throw("Expected PredictionTranscript id argument.") if(!$pt_id);
182 throw("Expected rank argument.") if(!$rank);
183
184 my $db = $self->db();
185
186 if($pexon->is_stored($db)) {
187 warning('PredictionExon is already stored in this DB.');
188 return $pexon->dbID();
189 }
190
191 if( ! $pexon->start || ! $pexon->end ||
192 ! $pexon->strand || ! defined $pexon->phase ) {
193 throw("PredictionExon does not have all attributes to store.\n" .
194 "start, end, strand and phase attributes must be set.");
195 }
196
197 #maintain reference to original passed-in prediction exon
198 my $original = $pexon;
199 my $seq_region_id;
200 ($pexon, $seq_region_id) = $self->_pre_store($pexon);
201
202 my $sth = $db->dbc->prepare
203 ("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " .
204 "seq_region_id, seq_region_start, seq_region_end, " .
205 "seq_region_strand, start_phase, score, p_value) " .
206 "VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ? )");
207
208 $sth->bind_param(1,$pt_id,SQL_INTEGER);
209 $sth->bind_param(2,$rank,SQL_SMALLINT);
210 $sth->bind_param(3,$seq_region_id,SQL_INTEGER);
211 $sth->bind_param(4,$pexon->start,SQL_INTEGER);
212 $sth->bind_param(5,$pexon->end,SQL_INTEGER);
213 $sth->bind_param(6,$pexon->strand,SQL_TINYINT);
214 $sth->bind_param(7,$pexon->phase,SQL_TINYINT);
215 $sth->bind_param(8,$pexon->score,SQL_DOUBLE);
216 $sth->bind_param(9,$pexon->p_value,SQL_DOUBLE);
217
218 $sth->execute();
219
220 my $dbID = $sth->{'mysql_insertid'};
221
222 #set the adaptor and dbID of the object they passed in
223 $original->dbID($dbID);
224 $original->adaptor($self);
225
226 return $dbID;
227 }
228
229
230
231 =head2 remove
232
233 Arg [1] : Bio::EnsEMBL::PredictionExon $exon
234 the exon to remove from the database
235 Example : $exon_adaptor->remove($exon);
236 Description: Removes an exon from the database
237 Returntype : none
238 Exceptions : none
239 Caller : general
240 Status : Stable
241
242 =cut
243
244 sub remove {
245 my $self = shift;
246 my $pexon = shift;
247
248 my $db = $self->db();
249
250 if(!$pexon->is_stored($db)) {
251 warning('PredictionExon is not in this DB - not removing');
252 return undef;
253 }
254
255 my $sth = $self->prepare(
256 "DELETE FROM prediction_exon WHERE prediction_exon_id = ?");
257 $sth->bind_param( 1, $pexon->dbID, SQL_INTEGER );
258 $sth->execute();
259
260 $pexon->dbID(undef);
261 $pexon->adaptor(undef);
262 }
263
264
265
266 =head2 list_dbIDs
267
268 Arg [1] : none
269 Example : @exon_ids = @{$exon_adaptor->list_dbIDs()};
270 Description: Gets an array of internal ids for all exons in the current db
271 Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
272 Returntype : list of ints
273 Exceptions : none
274 Caller : ?
275 Status : Stable
276
277 =cut
278
279 sub list_dbIDs {
280 my ($self,$ordered) = @_;
281
282 return $self->_list_dbIDs("prediction_exon",undef, $ordered);
283 }
284
285
286
287 #_objs_from_sth
288
289 # Arg [1] : Hashreference $hashref
290 # Example : none
291 # Description: PROTECTED implementation of abstract superclass method.
292 # responsible for the creation of Genes
293 # Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
294 # Exceptions : none
295 # Caller : internal
296 #
297
298 sub _objs_from_sth {
299 my ($self, $sth, $mapper, $dest_slice) = @_;
300
301 #
302 # This code is ugly because an attempt has been made to remove as many
303 # function calls as possible for speed purposes. Thus many caches and
304 # a fair bit of gymnastics is used.
305 #
306 my $sa = $self->db()->get_SliceAdaptor();
307
308 my @exons;
309 my %slice_hash;
310 my %sr_name_hash;
311 my %sr_cs_hash;
312
313 my($prediction_exon_id,$seq_region_id,
314 $seq_region_start, $seq_region_end, $seq_region_strand,
315 $start_phase, $score, $p_value);
316
317 $sth->bind_columns(\$prediction_exon_id,\$seq_region_id,
318 \$seq_region_start, \$seq_region_end, \$seq_region_strand,
319 \$start_phase, \$score, \$p_value);
320
321 my $asm_cs;
322 my $cmp_cs;
323 my $asm_cs_vers;
324 my $asm_cs_name;
325 my $cmp_cs_vers;
326 my $cmp_cs_name;
327 if($mapper) {
328 $asm_cs = $mapper->assembled_CoordSystem();
329 $cmp_cs = $mapper->component_CoordSystem();
330 $asm_cs_name = $asm_cs->name();
331 $asm_cs_vers = $asm_cs->version();
332 $cmp_cs_name = $cmp_cs->name();
333 $cmp_cs_vers = $cmp_cs->version();
334 }
335
336 my $dest_slice_start;
337 my $dest_slice_end;
338 my $dest_slice_strand;
339 my $dest_slice_length;
340 my $dest_slice_cs;
341 my $asma;
342 my $dest_slice_sr_name;
343 my $dest_slice_sr_id;
344
345 if($dest_slice) {
346 $dest_slice_start = $dest_slice->start();
347 $dest_slice_end = $dest_slice->end();
348 $dest_slice_strand = $dest_slice->strand();
349 $dest_slice_length = $dest_slice->length();
350 $dest_slice_cs = $dest_slice->coord_system;
351 $dest_slice_sr_name = $dest_slice->seq_region_name();
352 $dest_slice_sr_id = $dest_slice->get_seq_region_id();
353 $asma = $self->db->get_AssemblyMapperAdaptor();
354 }
355
356 FEATURE: while($sth->fetch()) {
357 #need to get the internal_seq_region, if present
358 $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
359 my $slice = $slice_hash{"ID:".$seq_region_id};
360 my $dest_mapper = $mapper;
361
362
363 if(!$slice) {
364 $slice = $sa->fetch_by_seq_region_id($seq_region_id);
365 $slice_hash{"ID:".$seq_region_id} = $slice;
366 $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
367 $sr_cs_hash{$seq_region_id} = $slice->coord_system();
368 }
369
370 #obtain a mapper if none was defined, but a dest_seq_region was
371 if(!$dest_mapper && $dest_slice &&
372 !$dest_slice_cs->equals($slice->coord_system)) {
373 $dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs,
374 $slice->coord_system);
375 $asm_cs = $dest_mapper->assembled_CoordSystem();
376 $cmp_cs = $dest_mapper->component_CoordSystem();
377 $asm_cs_name = $asm_cs->name();
378 $asm_cs_vers = $asm_cs->version();
379 $cmp_cs_name = $cmp_cs->name();
380 $cmp_cs_vers = $cmp_cs->version();
381 }
382
383 my $sr_name = $sr_name_hash{$seq_region_id};
384 my $sr_cs = $sr_cs_hash{$seq_region_id};
385
386 #
387 # remap the feature coordinates to another coord system
388 # if a mapper was provided
389 #
390 if($dest_mapper) {
391
392 if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
393 ( $seq_region_id, $seq_region_start,
394 $seq_region_end, $seq_region_strand )
395 =
396 $dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
397 $seq_region_strand, $sr_cs, 1, $dest_slice);
398
399 } else {
400
401 ( $seq_region_id, $seq_region_start,
402 $seq_region_end, $seq_region_strand )
403 = $dest_mapper->fastmap( $sr_name, $seq_region_start,
404 $seq_region_end, $seq_region_strand,
405 $sr_cs );
406 }
407
408 #skip features that map to gaps or coord system boundaries
409 next FEATURE if(!defined($seq_region_id));
410
411 #get a slice in the coord system we just mapped to
412 # if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
413 $slice = $slice_hash{"ID:".$seq_region_id} ||=
414 $sa->fetch_by_seq_region_id($seq_region_id);
415 # } else {
416 # $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
417 # $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
418 # $asm_cs_vers);
419 # }
420 }
421
422 #
423 # If a destination slice was provided convert the coords
424 # If the dest_slice starts at 1 and is foward strand, nothing needs doing
425 #
426 if($dest_slice) {
427 if($dest_slice_start != 1 || $dest_slice_strand != 1) {
428 if($dest_slice_strand == 1) {
429 $seq_region_start = $seq_region_start - $dest_slice_start + 1;
430 $seq_region_end = $seq_region_end - $dest_slice_start + 1;
431 } else {
432 my $tmp_seq_region_start = $seq_region_start;
433 $seq_region_start = $dest_slice_end - $seq_region_end + 1;
434 $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
435 $seq_region_strand *= -1;
436 }
437 }
438
439 #throw away features off the end of the requested slice
440 if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
441 ( $dest_slice_sr_id ne $seq_region_id )) {
442 next FEATURE;
443 }
444
445 $slice = $dest_slice;
446 }
447
448 # Finally, create the new PredictionExon.
449 push( @exons,
450 $self->_create_feature( 'Bio::EnsEMBL::PredictionExon', {
451 '-start' => $seq_region_start,
452 '-end' => $seq_region_end,
453 '-strand' => $seq_region_strand,
454 '-adaptor' => $self,
455 '-slice' => $slice,
456 '-dbID' => $prediction_exon_id,
457 '-phase' => $start_phase,
458 '-score' => $score,
459 '-p_value' => $p_value
460 } ) );
461
462 }
463
464 return \@exons;
465 }
466
467
468 1;