0
|
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::MiscFeatureAdaptor
|
|
24
|
|
25 =head1 SYNOPSIS
|
|
26
|
|
27 $mfa = $database_adaptor->get_MiscFeatureAdaptor();
|
|
28
|
|
29 # retrieve a misc feature by its dbID
|
|
30 my $misc_feat = $mfa->fetch_by_dbID(1234);
|
|
31
|
|
32 # retrieve all misc features in a given region
|
|
33 my @misc_feats = @{ $mfa->fetch_all_by_Slice($slice) };
|
|
34
|
|
35 # retrieve all misc features in a given region with a given set code
|
|
36 my @misc_clones =
|
|
37 @{ $mfa->fetch_all_by_Slice_and_set_code('cloneset') };
|
|
38
|
|
39 # store some misc features in the database
|
|
40 $mfa->store(@misc_features);
|
|
41
|
|
42 =head1 DESCRIPTION
|
|
43
|
|
44 This is an adaptor for the retrieval and storage of MiscFeatures.
|
|
45 Misc Features are extremely generic features that can be added with
|
|
46 minimal effort to the database. Currently misc features are used to
|
|
47 describe the locations of clone sets and tiling path information,
|
|
48 but arbitrary features can be stored. Misc features are grouped
|
|
49 into sets and can be fetched according to their grouping using the
|
|
50 fetch_all_by_Slice_and_set_code and fetch_all_by_set_code methods.
|
|
51 MiscFeatures may belong to more than one set.
|
|
52
|
|
53 =head1 METHODS
|
|
54
|
|
55 =cut
|
|
56
|
|
57 package Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor;
|
|
58
|
|
59 use strict;
|
|
60 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
|
|
61 use Bio::EnsEMBL::MiscFeature;
|
|
62 use Bio::EnsEMBL::Attribute;
|
|
63 use Bio::EnsEMBL::MiscSet;
|
|
64 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
|
|
65
|
|
66 use vars qw(@ISA);
|
|
67
|
|
68 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
|
|
69
|
|
70
|
|
71
|
|
72 =head2 fetch_all_by_Slice_and_set_code
|
|
73
|
|
74 Arg [1] : Bio::EnsEMBL::Slice $slice
|
|
75 A slice representing the region to fetch from
|
|
76 Arg [2...] : string $set_code
|
|
77 The code of the set to retrieve features from
|
|
78 Example : @feats = @{$mfa->fetch_all_by_Slice_and_set_code('cloneset')};
|
|
79 Description: Retrieves a set of MiscFeatures which have a particular set code
|
|
80 and which lie in a particular region. All features with the
|
|
81 provide set code and which overlap the given slice are returned.
|
|
82 Returntype : listref of Bio::EnsEMBL::MiscFeatures
|
|
83 Exceptions : throw if set_code is not provided
|
|
84 warning if no set for provided set code exists
|
|
85 Caller : general
|
|
86 Status : Stable
|
|
87
|
|
88 =cut
|
|
89
|
|
90 sub fetch_all_by_Slice_and_set_code {
|
|
91 my $self = shift;
|
|
92 my $slice = shift;
|
|
93
|
|
94 throw('Set code argument is required.') unless @_;
|
|
95
|
|
96 my $msa = $self->db->get_MiscSetAdaptor();
|
|
97 my @sets = ();
|
|
98 my $max_len = 0;
|
|
99 foreach my $set_code (@_) {
|
|
100 my $set = $msa->fetch_by_code($set_code);
|
|
101 if($set) {
|
|
102 $max_len = $set->longest_feature if $set->longest_feature > $max_len;
|
|
103 push @sets, $set->dbID;
|
|
104 } else {
|
|
105 warning("No misc_set with code [$set_code] exists");
|
|
106 }
|
|
107 }
|
|
108 my $constraint;
|
|
109 if( @sets > 1 ) {
|
|
110 $constraint = " mfms.misc_set_id in ( @{[join ',',@sets]} ) ";
|
|
111 } elsif( @sets == 1 ) {
|
|
112 $constraint = " mfms.misc_set_id = $sets[0] ";
|
|
113 } else {
|
|
114 return [];
|
|
115 }
|
|
116
|
|
117 $self->_max_feature_length($max_len);
|
|
118
|
|
119 my $results = $self->fetch_all_by_Slice_constraint($slice, $constraint);
|
|
120
|
|
121 $self->_max_feature_length(undef);
|
|
122
|
|
123 return $results;
|
|
124 }
|
|
125
|
|
126
|
|
127
|
|
128 =head2 fetch_all_by_attribute_type_value
|
|
129
|
|
130 Arg [1] : string $attrib_type_code
|
|
131 The code of the attribute type to fetch features for
|
|
132 Arg [2] : (optional) string $attrib_value
|
|
133 The value of the attribute to fetch features for
|
|
134 Example :
|
|
135 #get all misc features that have an embl accession
|
|
136 @feats = @{$mfa->fetch_all_by_attrib_type_value('embl_acc')};
|
|
137 #get the misc feature with synonym 'AL014121'
|
|
138 ($feat)=@{$mfa->fetch_all_by_attrib_type_value('synonym','AL014121');
|
|
139 Description: Retrieves MiscFeatures which have a particular attribute.
|
|
140 If the attribute value argument is also provided only
|
|
141 features which have the attribute AND a particular value
|
|
142 are returned. The features are returned in their native
|
|
143 coordinate system (i.e. the coordinate system that they
|
|
144 are stored in).
|
|
145 Returntype : listref of Bio::EnsEMBL::MiscFeatures
|
|
146 Exceptions : throw if attrib_type code arg is not provided
|
|
147 Caller : general
|
|
148 Status : Stable
|
|
149
|
|
150 =cut
|
|
151
|
|
152 sub fetch_all_by_attribute_type_value {
|
|
153 my $self = shift;
|
|
154 my $attrib_type_code = shift;
|
|
155 my $attrib_value = shift;
|
|
156
|
|
157 throw("Attrib type code argument is required.")
|
|
158 if ( !$attrib_type_code );
|
|
159
|
|
160 # Need to do 2 queries so that all of the ids come back with the
|
|
161 # features. The problem with adding attrib constraints to filter the
|
|
162 # misc_features which come back is that not all of the attributes will
|
|
163 # come back
|
|
164
|
|
165 my $sql = qq(
|
|
166 SELECT DISTINCT
|
|
167 ma.misc_feature_id
|
|
168 FROM misc_attrib ma,
|
|
169 attrib_type at,
|
|
170 misc_feature mf,
|
|
171 seq_region sr,
|
|
172 coord_system cs
|
|
173 WHERE ma.attrib_type_id = at.attrib_type_id
|
|
174 AND at.code = ?
|
|
175 AND ma.misc_feature_id = mf.misc_feature_id
|
|
176 AND mf.seq_region_id = sr.seq_region_id
|
|
177 AND sr.coord_system_id = cs.coord_system_id
|
|
178 AND cs.species_id = ?);
|
|
179
|
|
180 if ($attrib_value) {
|
|
181 $sql .= " AND ma.value = ?";
|
|
182 }
|
|
183
|
|
184 my $sth = $self->prepare($sql);
|
|
185
|
|
186 $sth->bind_param( 1, $attrib_type_code, SQL_VARCHAR );
|
|
187 $sth->bind_param( 2, $self->species_id(), SQL_INTEGER );
|
|
188 if ($attrib_value) {
|
|
189 $sth->bind_param( 3, $attrib_value, SQL_VARCHAR );
|
|
190 }
|
|
191
|
|
192 $sth->execute();
|
|
193
|
|
194 my @ids = map { $_->[0] } @{ $sth->fetchall_arrayref() };
|
|
195
|
|
196 $sth->finish();
|
|
197
|
|
198 # Construct constraints from the list of ids. Split ids into groups
|
|
199 # of 1000 to ensure that the query is not too big.
|
|
200 my @constraints;
|
|
201 while (@ids) {
|
|
202 my @subset = splice( @ids, 0, 1000 );
|
|
203 if ( @subset == 1 ) {
|
|
204 push @constraints, "mf.misc_feature_id = $subset[0]";
|
|
205 } else {
|
|
206 my $id_str = join( ',', @subset );
|
|
207 push @constraints, "mf.misc_feature_id in ($id_str)";
|
|
208 }
|
|
209 }
|
|
210
|
|
211 my @results;
|
|
212 foreach my $constraint (@constraints) {
|
|
213 push @results, @{ $self->generic_fetch($constraint) };
|
|
214 }
|
|
215
|
|
216 return \@results;
|
|
217 } ## end sub fetch_all_by_attribute_type_value
|
|
218
|
|
219
|
|
220 #_tables
|
|
221 #
|
|
222 # Arg [1] : none
|
|
223 # Example : none
|
|
224 # Description: PROTECTED Implementation of abstract superclass method to
|
|
225 # provide the name of the tables to query
|
|
226 # Returntype : string
|
|
227 # Exceptions : none
|
|
228 # Caller : internal
|
|
229
|
|
230
|
|
231 sub _tables {
|
|
232 my $self = shift;
|
|
233
|
|
234 return (['misc_feature', 'mf'],
|
|
235 ['misc_feature_misc_set', 'mfms'],
|
|
236 ['misc_attrib', 'ma'],
|
|
237 ['attrib_type', 'at']);
|
|
238 }
|
|
239
|
|
240
|
|
241 #_columns
|
|
242
|
|
243 # Arg [1] : none
|
|
244 # Example : none
|
|
245 # Description: PROTECTED Implementation of abstract superclass method to
|
|
246 # provide the name of the columns to query
|
|
247 # Returntype : list of strings
|
|
248 # Exceptions : none
|
|
249 # Caller : internal
|
|
250
|
|
251 sub _columns {
|
|
252 my $self = shift;
|
|
253
|
|
254 #warning _objs_from_sth implementation depends on ordering
|
|
255 return qw (mf.misc_feature_id
|
|
256 mf.seq_region_id
|
|
257 mf.seq_region_start
|
|
258 mf.seq_region_end
|
|
259 mf.seq_region_strand
|
|
260 ma.value
|
|
261 at.code
|
|
262 mfms.misc_set_id
|
|
263 at.name
|
|
264 at.description);
|
|
265 }
|
|
266
|
|
267
|
|
268
|
|
269 # _default_where_clause
|
|
270
|
|
271 # Arg [1] : none
|
|
272 # Example : none
|
|
273 # Description: Overrides superclass method to provide an additional
|
|
274 # table joining constraint before the SQL query is performed.
|
|
275 # Returntype : string
|
|
276 # Exceptions : none
|
|
277 # Caller : generic_fetch
|
|
278
|
|
279 sub _default_where_clause {
|
|
280 my $self = shift;
|
|
281
|
|
282 return '';
|
|
283 }
|
|
284
|
|
285
|
|
286 sub _left_join {
|
|
287 my $self = shift;
|
|
288
|
|
289 return(
|
|
290 ['misc_feature_misc_set','mf.misc_feature_id = mfms.misc_feature_id'],
|
|
291 ['misc_attrib', 'mf.misc_feature_id = ma.misc_feature_id'],
|
|
292 ['attrib_type','ma.attrib_type_id = at.attrib_type_id']);
|
|
293 }
|
|
294
|
|
295
|
|
296 sub _final_clause {
|
|
297 my $self = shift;
|
|
298
|
|
299 return " ORDER BY mf.misc_feature_id";
|
|
300 }
|
|
301
|
|
302
|
|
303 # _objs_from_sth
|
|
304
|
|
305 # Arg [1] : StatementHandle $sth
|
|
306 # Example : none
|
|
307 # Description: PROTECTED implementation of abstract superclass method.
|
|
308 # responsible for the creation of MiscFeatures from a
|
|
309 # hashref generated from an SQL query
|
|
310 # Returntype : listref of Bio::EnsEMBL::MiscFeatures
|
|
311 # Exceptions : none
|
|
312 # Caller : internal
|
|
313
|
|
314 sub _objs_from_sth {
|
|
315 my ($self, $sth, $mapper, $dest_slice) = @_;
|
|
316
|
|
317 #
|
|
318 # This code is ugly because an attempt has been made to remove as many
|
|
319 # function calls as possible for speed purposes. Thus many caches and
|
|
320 # a fair bit of gymnastics is used.
|
|
321 #
|
|
322
|
|
323 my $sa = $self->db()->get_SliceAdaptor();
|
|
324 my $msa = $self->db->get_MiscSetAdaptor();
|
|
325
|
|
326 my @features;
|
|
327 my %ms_hash;
|
|
328 my %slice_hash;
|
|
329 my %sr_name_hash;
|
|
330 my %sr_cs_hash;
|
|
331
|
|
332 my($misc_feature_id, $seq_region_id, $seq_region_start, $seq_region_end,
|
|
333 $seq_region_strand, $attrib_value, $attrib_type_code, $misc_set_id,
|
|
334 $attrib_type_name, $attrib_type_description );
|
|
335
|
|
336 $sth->bind_columns( \$misc_feature_id, \$seq_region_id, \$seq_region_start,
|
|
337 \$seq_region_end, \$seq_region_strand,
|
|
338 \$attrib_value, \$attrib_type_code,\$misc_set_id,
|
|
339 \$attrib_type_name, \$attrib_type_description );
|
|
340
|
|
341 my $asm_cs;
|
|
342 my $cmp_cs;
|
|
343 my $asm_cs_vers;
|
|
344 my $asm_cs_name;
|
|
345 my $cmp_cs_vers;
|
|
346 my $cmp_cs_name;
|
|
347 if($mapper) {
|
|
348 $asm_cs = $mapper->assembled_CoordSystem();
|
|
349 $cmp_cs = $mapper->component_CoordSystem();
|
|
350 $asm_cs_name = $asm_cs->name();
|
|
351 $asm_cs_vers = $asm_cs->version();
|
|
352 $cmp_cs_name = $cmp_cs->name();
|
|
353 $cmp_cs_vers = $cmp_cs->version();
|
|
354 }
|
|
355
|
|
356 my $dest_slice_start;
|
|
357 my $dest_slice_end;
|
|
358 my $dest_slice_strand;
|
|
359 my $dest_slice_length;
|
|
360 my $dest_slice_sr_name;
|
|
361 my $dest_slice_sr_id;
|
|
362 if($dest_slice) {
|
|
363 $dest_slice_start = $dest_slice->start();
|
|
364 $dest_slice_end = $dest_slice->end();
|
|
365 $dest_slice_strand = $dest_slice->strand();
|
|
366 $dest_slice_length = $dest_slice->length();
|
|
367 $dest_slice_sr_name = $dest_slice->seq_region_name();
|
|
368 $dest_slice_sr_id = $dest_slice->get_seq_region_id();
|
|
369 }
|
|
370
|
|
371 my $current = -1;
|
|
372 my $throw_away = -1;
|
|
373 my $feat;
|
|
374 my $feat_misc_sets;
|
|
375 my $feat_attribs;
|
|
376 my $seen_attribs;
|
|
377
|
|
378 FEATURE: while($sth->fetch()) {
|
|
379 #if this feature is not being used, skip all rows related to it
|
|
380 next if($throw_away == $misc_feature_id);
|
|
381
|
|
382 if ($current == $misc_feature_id) {
|
|
383 #still working on building up attributes and sets for current feature
|
|
384
|
|
385 #if there is a misc_set, add it to the current feature
|
|
386 if ($misc_set_id) {
|
|
387 my $misc_set = $ms_hash{$misc_set_id} ||=
|
|
388 $msa->fetch_by_dbID($misc_set_id);
|
|
389 if ( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
|
|
390 $feat->add_MiscSet( $misc_set );
|
|
391 $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
|
|
392 }
|
|
393 }
|
|
394
|
|
395 #if there is a new attribute add it to the current feature
|
|
396 if ($attrib_value && $attrib_type_code &&
|
|
397 !$seen_attribs->{"$attrib_type_code:$attrib_value"}) {
|
|
398 my $attrib = Bio::EnsEMBL::Attribute->new
|
|
399 ( -CODE => $attrib_type_code,
|
|
400 -NAME => $attrib_type_name,
|
|
401 -DESC => $attrib_type_description,
|
|
402 -VALUE => $attrib_value
|
|
403 );
|
|
404
|
|
405
|
|
406 $feat_attribs ||= [];
|
|
407 push @$feat_attribs, $attrib;
|
|
408 $seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
|
|
409 }
|
|
410
|
|
411 } else {
|
|
412 if ($feat) {
|
|
413 #start working on a new feature, discard references to last one
|
|
414 $feat = {};
|
|
415 $feat_attribs = [];
|
|
416 $feat_misc_sets = {};
|
|
417 $seen_attribs = {};
|
|
418 }
|
|
419
|
|
420 $current = $misc_feature_id;
|
|
421 #need to get the internal_seq_region, if present
|
|
422 $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
|
|
423 my $slice = $slice_hash{"ID:".$seq_region_id};
|
|
424
|
|
425 if (!$slice) {
|
|
426 $slice = $sa->fetch_by_seq_region_id($seq_region_id);
|
|
427 $slice_hash{"ID:".$seq_region_id} = $slice;
|
|
428 $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
|
|
429 $sr_cs_hash{$seq_region_id} = $slice->coord_system();
|
|
430 }
|
|
431
|
|
432 my $sr_name = $sr_name_hash{$seq_region_id};
|
|
433 my $sr_cs = $sr_cs_hash{$seq_region_id};
|
|
434 #
|
|
435 # remap the feature coordinates to another coord system
|
|
436 # if a mapper was provided
|
|
437 #
|
|
438 if ($mapper) {
|
|
439
|
|
440
|
|
441 if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
|
|
442 ( $seq_region_id, $seq_region_start,$seq_region_end, $seq_region_strand ) =
|
|
443 $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
|
|
444 $seq_region_strand, $sr_cs, 1, $dest_slice);
|
|
445
|
|
446 } else {
|
|
447
|
|
448 ( $seq_region_id, $seq_region_start,$seq_region_end, $seq_region_strand ) =
|
|
449 $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,$seq_region_strand, $sr_cs );
|
|
450 }
|
|
451
|
|
452 #skip features that map to gaps or coord system boundaries
|
|
453 if(!defined($seq_region_id)) {
|
|
454 $throw_away = $misc_feature_id;
|
|
455 next FEATURE;
|
|
456 }
|
|
457
|
|
458 #get a slice in the coord system we just mapped to
|
|
459 # if ($asm_cs == $sr_cs ||
|
|
460 # ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
|
|
461 $slice = $slice_hash{"ID:".$seq_region_id} ||=
|
|
462 $sa->fetch_by_seq_region_id($seq_region_id);
|
|
463 # } else {
|
|
464 # $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
|
|
465 # $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
|
|
466 # $asm_cs_vers);
|
|
467 # }
|
|
468 }
|
|
469
|
|
470 #
|
|
471 # If a destination slice was provided convert the coords
|
|
472 # If the dest_slice starts at 1 and is foward strand, nothing needs doing
|
|
473 #
|
|
474 if ($dest_slice) {
|
|
475 if ($dest_slice_start != 1 || $dest_slice_strand != 1) {
|
|
476 if ($dest_slice_strand == 1) {
|
|
477 $seq_region_start = $seq_region_start - $dest_slice_start + 1;
|
|
478 $seq_region_end = $seq_region_end - $dest_slice_start + 1;
|
|
479 } else {
|
|
480 my $tmp_seq_region_start = $seq_region_start;
|
|
481 $seq_region_start = $dest_slice_end - $seq_region_end + 1;
|
|
482 $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
|
|
483 $seq_region_strand *= -1;
|
|
484 }
|
|
485 }
|
|
486 #throw away features off the end of the requested slice
|
|
487 if ($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
|
|
488 ( $dest_slice_sr_id ne $seq_region_id )) {
|
|
489 #flag this feature as one to throw away
|
|
490 $throw_away = $misc_feature_id;
|
|
491 next FEATURE;
|
|
492 }
|
|
493 $slice = $dest_slice;
|
|
494 }
|
|
495
|
|
496
|
|
497 if ($attrib_value && $attrib_type_code) {
|
|
498 my $attrib = Bio::EnsEMBL::Attribute->new
|
|
499 ( -CODE => $attrib_type_code,
|
|
500 -NAME => $attrib_type_name,
|
|
501 -DESC => $attrib_type_description,
|
|
502 -VALUE => $attrib_value
|
|
503 );
|
|
504 $feat_attribs = [$attrib];
|
|
505 $seen_attribs->{"$attrib_type_code:$attrib_value"} = 1;
|
|
506 }
|
|
507
|
|
508 $feat =
|
|
509 $self->_create_feature_fast( 'Bio::EnsEMBL::MiscFeature', {
|
|
510 'start' => $seq_region_start,
|
|
511 'end' => $seq_region_end,
|
|
512 'strand' => $seq_region_strand,
|
|
513 'slice' => $slice,
|
|
514 'adaptor' => $self,
|
|
515 'dbID' => $misc_feature_id,
|
|
516 'attributes' => $feat_attribs
|
|
517 } );
|
|
518
|
|
519 push @features, $feat;
|
|
520
|
|
521 if ($misc_set_id) {
|
|
522 #get the misc_set object
|
|
523 my $misc_set = $ms_hash{$misc_set_id} ||=
|
|
524 $msa->fetch_by_dbID($misc_set_id);
|
|
525 if ( ! exists $feat_misc_sets->{$misc_set->{'code'}} ) {
|
|
526 $feat->add_MiscSet( $misc_set );
|
|
527 $feat_misc_sets->{$misc_set->{'code'}} = $misc_set;
|
|
528 }
|
|
529 }
|
|
530 }
|
|
531 }
|
|
532
|
|
533 return \@features;
|
|
534 }
|
|
535
|
|
536
|
|
537
|
|
538 =head2 list_dbIDs
|
|
539
|
|
540 Arg [1] : none
|
|
541 Example : @feature_ids = @{$misc_feature_adaptor->list_dbIDs()};
|
|
542 Description: Gets an array of internal ids for all misc_features in the
|
|
543 current db
|
|
544 Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
|
|
545 Returntype : list of ints
|
|
546 Exceptions : none
|
|
547 Caller : ?
|
|
548 Status : Stable
|
|
549
|
|
550 =cut
|
|
551
|
|
552 sub list_dbIDs {
|
|
553 my ($self,$ordered) = @_;
|
|
554
|
|
555 return $self->_list_dbIDs("misc_feature",undef,$ordered);
|
|
556 }
|
|
557
|
|
558
|
|
559 =head2 store
|
|
560
|
|
561 Arg [1] : list of Bio::EnsEMBL::MiscFeatures @misc_features
|
|
562 Example : $misc_feature_adaptor->store(@misc_features);
|
|
563 Description: Stores a list of MiscFeatures in this database. The stored
|
|
564 features will have their
|
|
565 Returntype : none
|
|
566 Exceptions : throw on invalid arguments
|
|
567 warning if misc feature is already stored in this database
|
|
568 throw if start/end/strand attribs are not valid
|
|
569 Caller : general
|
|
570 Status : Stable
|
|
571
|
|
572 =cut
|
|
573
|
|
574 sub store {
|
|
575 my $self = shift;
|
|
576 my @misc_features = @_;
|
|
577
|
|
578 my $db = $self->db();
|
|
579
|
|
580 my $feature_sth = $self->prepare
|
|
581 ("INSERT INTO misc_feature SET " .
|
|
582 " seq_region_id = ?, " .
|
|
583 " seq_region_start = ?, " .
|
|
584 " seq_region_end = ?, " .
|
|
585 " seq_region_strand = ?");
|
|
586
|
|
587 my $feature_set_sth = $self->prepare
|
|
588 ("INSERT IGNORE misc_feature_misc_set SET " .
|
|
589 " misc_feature_id = ?, " .
|
|
590 " misc_set_id = ?");
|
|
591
|
|
592 my $msa = $db->get_MiscSetAdaptor();
|
|
593 my $aa = $db->get_AttributeAdaptor();
|
|
594
|
|
595 FEATURE:
|
|
596 foreach my $mf (@misc_features) {
|
|
597 if(!ref($mf) || !$mf->isa('Bio::EnsEMBL::MiscFeature')) {
|
|
598 throw("List of MiscFeature arguments expeceted");
|
|
599 }
|
|
600
|
|
601 if($mf->is_stored($db)) {
|
|
602 warning("MiscFeature [" .$mf->dbID."] is already stored in database.");
|
|
603 next FEATURE;
|
|
604 }
|
|
605
|
|
606 # do some checking of the start/end and convert to seq_region coords
|
|
607 my $original = $mf;
|
|
608 my $seq_region_id;
|
|
609 ($mf, $seq_region_id) = $self->_pre_store($mf);
|
|
610
|
|
611 # store the actual MiscFeature
|
|
612 $feature_sth->bind_param(1,$seq_region_id,SQL_INTEGER);
|
|
613 $feature_sth->bind_param(2,$mf->start,SQL_INTEGER);
|
|
614 $feature_sth->bind_param(3,$mf->end,SQL_INTEGER);
|
|
615 $feature_sth->bind_param(4,$mf->strand,SQL_TINYINT);
|
|
616 $feature_sth->execute();
|
|
617
|
|
618 my $dbID = $feature_sth->{'mysql_insertid'};
|
|
619
|
|
620 $mf->dbID($dbID);
|
|
621 $mf->adaptor($self);
|
|
622
|
|
623 # store all the attributes
|
|
624 my $attribs = $mf->get_all_Attributes();
|
|
625 $aa->store_on_MiscFeature($mf, $attribs);
|
|
626
|
|
627 # store all the sets that have not been stored yet
|
|
628 my $sets = $mf->get_all_MiscSets();
|
|
629 foreach my $set (@$sets) {
|
|
630 $msa->store($set) if(!$set->is_stored($db));
|
|
631
|
|
632 # update the misc_feat_misc_set table to store the set relationship
|
|
633 $feature_set_sth->bind_param(1,$dbID,SQL_INTEGER);
|
|
634 $feature_set_sth->bind_param(2,$set->dbID,SQL_INTEGER);
|
|
635
|
|
636 $feature_set_sth->execute();
|
|
637 }
|
|
638 }
|
|
639
|
|
640 return;
|
|
641 }
|
|
642
|
|
643 1;
|
|
644
|
|
645
|
|
646
|
|
647
|
|
648
|