SliceAdaptor.pm 50.1 KB
Newer Older
1 2

#
Simon Potter's avatar
pod  
Simon Potter committed
3
# Ensembl module for Bio::EnsEMBL::DBSQL::SliceAdaptor
4 5
#
#
Graham McVicker's avatar
Graham McVicker committed
6
# Copyright (c) 2004 Ensembl
7 8 9 10 11 12 13
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

14 15
Bio::EnsEMBL::DBSQL::SliceAdaptor - A database aware adaptor responsible for
the creation of Slice objects.
16 17 18

=head1 SYNOPSIS

Graham McVicker's avatar
Graham McVicker committed
19 20
  use Bio::EnsEMBL::DBSQL::DBAdaptor;
  use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
21

Graham McVicker's avatar
Graham McVicker committed
22
  $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
23

Graham McVicker's avatar
Graham McVicker committed
24
  $slice_adaptor = $db->get_SliceAdaptor();
25

Graham McVicker's avatar
Graham McVicker committed
26 27 28 29 30
  # get a slice on the entire chromosome X
  $chr_slice = $slice_adaptor->fetch_by_region('chromosome','X');

  # get a slice for each clone in the database
  foreach $cln_slice (@{$slice_adaptor->fetch_all('clone')}) {
31 32 33
    #do something with clone
  }

Graham McVicker's avatar
Graham McVicker committed
34 35
  # get a slice which is part of NT_004321
  $spctg_slice = $slice_adaptor->fetch_by_region('supercontig','NT_004321',
36
                                                    200_000, 600_000);
37 38


Graham McVicker's avatar
Graham McVicker committed
39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69
  # get all non-redundant slices from the highest possible coordinate systems
  $slices = $slice_adaptor->fetch_all('toplevel');

  # include non-reference regions
  $slices = $slice_adaptor->fetch_all('toplevel',undef,1);

  # include non-duplicate regions
  $slices = $slice_adaptor->fetch_all('toplevel', undef, 0, 1);

  # split up a list of slices into smaller slices
  $overlap = 1000;
  $max_length = 1e6;
  $slices = split_Slices($slices, $max_length, $overlap);


  # store a list of slice names in a file
  open(FILE, ">$filename") or die("Could not open file $filename");
  foreach my $slice (@$slices) {
    print FILE $slice->name(), "\n";
  }
  close FILE;

  # retreive a list of slices from a file
  open(FILE, $filename) or die("Could not open file $filename");
  while($name = <FILE>) {
    chomp($name);
    $slice = $slice_adaptor->fetch_by_name($name);

    # do something with slice
  }

70 71
=head1 DESCRIPTION

72
This module is responsible for fetching Slices representing genomic regions
Graham McVicker's avatar
Graham McVicker committed
73
from a database.  A Details on how slices can be used are in the
74
Bio::EnsEMBL::Slice module.
75

76
=head1 CONTACT
77

Graham McVicker's avatar
Graham McVicker committed
78 79 80
This module is part of the Ensembl project http://www.ensembl.org

For more information email <ensembl-dev@ebi.ac.uk>
81

82
=head1 METHODS
83 84 85 86

=cut


87
package Bio::EnsEMBL::DBSQL::SliceAdaptor;
88 89 90
use vars qw(@ISA);
use strict;

91

92 93
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Slice;
94
use Bio::EnsEMBL::Mapper;
95

96
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
97

98

99
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
100

101 102
sub new {
  my $caller = shift;
103

104
  my $class = ref($caller) || $caller;
105

106
  my $self = $class->SUPER::new(@_);
107

108 109 110 111 112 113
  # use a cache which is shared and also used by the assembly
  # mapper adaptor
  my $seq_region_cache = $self->db->get_SeqRegionCache();

  $self->{'sr_name_cache'} = $seq_region_cache->{'name_cache'};
  $self->{'sr_id_cache'}   = $seq_region_cache->{'id_cache'};
114 115 116 117 118 119 120

  return $self;
}


=head2 fetch_by_region

121
  Arg [1]    : string $coord_system_name (optional)
122
               The name of the coordinate system of the slice to be created
123
               This may be a name of an actual coordinate system or an alias
124 125 126 127
               to a coordinate system.  Valid aliases are 'seqlevel' or
               'toplevel'.
  Arg [2]    : string $seq_region_name
               The name of the sequence region that the slice will be
Graham McVicker's avatar
Graham McVicker committed
128
               created on.
129 130 131 132 133 134 135 136
  Arg [3]    : int $start (optional, default = 1)
               The start of the slice on the sequence region
  Arg [4]    : int $end (optional, default = seq_region length)
               The end of the slice on the sequence region
  Arg [5]    : int $strand (optional, default = 1)
               The orientation of the slice on the sequence region
  Arg [6]    : string $version (optional, default = default version)
               The version of the coordinate system to use (e.g. NCBI33)
137 138 139
  Example    : $slice = $slice_adaptor->fetch_by_region('chromosome', 'X');
               $slice = $slice_adaptor->fetch_by_region('clone', 'AC008066.4');
  Description: Retrieves a slice on the requested region.  At a minimum the
140 141 142 143 144 145 146 147 148 149 150
               name the name of the seq_region to fetch must be provided.

               If no coordinate system name is provided than a slice on the
               highest ranked coordinate system with a matching
               seq_region_name will be returned.  If a version but no
               coordinate system name is provided, the same behaviour will
               apply, but only coordinate systems of the appropriate version
               are considered.  The same applies if the 'toplevel' coordinate
               system is specified, however in this case the version is
               ignored.  The coordinate system should always be specified if
               it is known, since this is unambiguous and faster.
151 152 153 154 155 156 157 158 159 160 161 162 163 164

               Some fuzzy matching is performed if no exact match for
               the provided name is found.  This allows clones to be
               fetched even when their version is not known.  For
               example fetch_by_region('clone', 'AC008066') will
               retrieve the sequence_region with name 'AC008066.4'.

               If the requested seq_region is not found in the database undef
               is returned.

  Returntype : Bio::EnsEMBL::Slice or undef
  Exceptions : throw if no seq_region_name is provided
               throw if invalid coord_system_name is provided
               throw if start > end is provided
165
  Caller     : general
166
  Status     : Stable
167 168 169

=cut

170 171 172 173

#
# ARNE: This subroutine needs simplification!! 
#
174 175 176 177
sub fetch_by_region {
  my ($self, $coord_system_name, $seq_region_name,
      $start, $end, $strand, $version) = @_;

178 179
  $start  = 1 if (!defined($start));
  $strand = 1 if (!defined($strand));
180

181
  throw('seq_region_name argument is required') if (!defined($seq_region_name));
182

183 184
  my $cs;
  my $csa = $self->db->get_CoordSystemAdaptor();
185

186
  if ($coord_system_name) {
187 188
    $cs = $csa->fetch_by_name($coord_system_name,$version);

189
    ## REMOVE THESE THREE LINES WHEN STICKLEBACK DB IS FIXED!
190 191 192 193
    if( !$cs && $coord_system_name eq 'chromosome' ) {
      $cs = $csa->fetch_by_name('group',$version);
    }

194
    if (!$cs) {
195 196 197 198 199
      throw("Unknown coordinate system:\n name='$coord_system_name' " .
            "version='$version'\n");
    }

    # fetching by toplevel is same as fetching w/o name or version
200
    if ($cs->is_top_level()) {
201 202 203
      $cs = undef;
      $version = undef;
    }
204
  }
205 206 207 208 209 210

  my $constraint;
  my $sql;
  my @bind_vals;
  my $key;

211
  if ($cs) {
212
 
213
    push @bind_vals, $cs->dbID();
214
    $sql = "SELECT sr.name, sr.seq_region_id, sr.length, " .
215 216
           $cs->dbID() ." FROM seq_region sr ";

217
	      $constraint = "sr.coord_system_id = ?";
218

219
    $key = "$seq_region_name:".$cs->dbID();
220 221 222 223 224 225 226 227 228 229
  } else {
    $sql = "SELECT sr.name, sr.seq_region_id, sr.length, " .
           "       cs.coord_system_id " .
           "FROM   seq_region sr, coord_system cs ";

    $constraint = "sr.coord_system_id = cs.coord_system_id ";
    if($version) {
      $constraint .= "AND cs.version = ? ";
      push @bind_vals, $version;
    }
230
    $constraint .= "ORDER BY cs.rank ASC";
231 232
  }

233
  # check the cache so we only go to the db if necessary
234
  my $length;
235
  my $arr;
236
  if ($key) {
237
    $arr = $self->{'sr_name_cache'}->{$key};
238
  }
239

240
  if ($arr) {
241
    $length = $arr->[3];
242
  } else {
243
    my $sth = $self->prepare($sql . " WHERE sr.name = ? AND " . $constraint);
244 245 246
    # Quotes around "$seq_region_name" are needed so that mysql does not
    # treat chromosomes like '6' as an int.  This was doing horrible
    # inexact matches like '6DR51', '6_UN', etc.
247
    $sth->bind_param(1, "$seq_region_name", SQL_VARCHAR);
248
    if ($cs){
249
	$sth->bind_param(2, $cs->dbID, SQL_INTEGER);
250 251
    }
    else{
252
	$sth->bind_param(2, $version, SQL_VARCHAR)  if ($version);	
253
    }
254 255

    $sth->execute();
256

257
    if ($sth->rows() == 0) {
258
      $sth->finish();
Graham McVicker's avatar
Graham McVicker committed
259

260 261
      # do fuzzy matching, assuming that we are just missing a version on
      # the end of the seq_region name
262
      
263
      $sth = $self->prepare($sql . " WHERE sr.name LIKE ? AND " . $constraint);
264

265
      $sth->bind_param(1, "$seq_region_name.%", SQL_VARCHAR);
266 267

      if ($cs){
268
	  $sth->bind_param(2, $cs->dbID, SQL_INTEGER);
269 270
      }
      else{
271
	  $sth->bind_param(2, $version, SQL_VARCHAR) if ($version);	
272
      }
273
      $sth->execute();
274 275

      my $prefix_len = length($seq_region_name) + 1;
276 277
      my $high_ver = undef;
      my $high_cs = $cs;
278 279 280 281

      # find the fuzzy-matched seq_region with the highest postfix (which ought
      # to be a version)

282 283 284
      my ($tmp_name, $id, $tmp_length, $cs_id);
      $sth->bind_columns(\$tmp_name, \$id, \$tmp_length, \$cs_id);

Felix Kokocinski's avatar
Felix Kokocinski committed
285
      my $i = 0;
286 287

      while ($sth->fetch) {
288
        my $tmp_cs = ($cs) ? $cs : $csa->fetch_by_dbID($cs_id);
289

290
        # cache values for future reference
291
        my $arr = [ $id, $tmp_name, $cs_id, $tmp_length ];
292 293
        $self->{'sr_name_cache'}->{"$tmp_name:$cs_id"} = $arr;
        $self->{'sr_id_cache'}->{"$id"} = $arr;
Graham McVicker's avatar
Graham McVicker committed
294

295
        my $tmp_ver = substr($tmp_name, $prefix_len);
296

297 298
        # skip versions which are non-numeric and apparently not versions
        next if($tmp_ver !~ /^\d+$/);
299

300 301 302 303 304 305 306 307
        # take version with highest num, if two versions match take one with
        # highest ranked coord system (lowest num)
        if(!defined($high_ver) || $tmp_ver > $high_ver ||
           ($tmp_ver == $high_ver && $tmp_cs->rank < $high_cs->rank)) {
            $seq_region_name = $tmp_name;
            $length          = $tmp_length;
            $high_ver        = $tmp_ver;
            $high_cs         = $tmp_cs;
Graham McVicker's avatar
Graham McVicker committed
308
        }
309 310

        $i++;
Graham McVicker's avatar
Graham McVicker committed
311
      }
312 313
      $sth->finish();

314 315 316 317 318
      # warn if fuzzy matching found more than one result
      if ($i > 1) {
        warning("Fuzzy matching of seq_region_name returned more than one result.\nYou might want to check whether the returned seq_region\n(".$high_cs->name.":$seq_region_name) is the one you intended to fetch.\n");
      }

319 320
      $cs = $high_cs;

321
      #return if we did not find any appropriate match:
322 323
      return undef if (!defined($high_ver));

324 325
    } else {

326 327
      my ($id, $cs_id);
      ($seq_region_name, $id, $length, $cs_id) = $sth->fetchrow_array();
328
      $sth->finish();
329

330 331
      # cahce to speed up for future queries
      my $arr = [ $id, $seq_region_name, $cs_id, $length ];
332 333
      $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
      $self->{'sr_id_cache'}->{"$id"} = $arr;
334 335

      $cs = $csa->fetch_by_dbID( $cs_id );
336
    }
337
  }
338

339
  $end = $length if(!defined($end));
Graham McVicker's avatar
Graham McVicker committed
340

341 342
  if($end+1 < $start) {
    throw("start [$start] must be less than or equal to end+1 [$end+1]");
343 344
  }

345
  return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM      => $cs,
346 347 348 349 350 351
                                  -SEQ_REGION_NAME   => $seq_region_name,
                                  -SEQ_REGION_LENGTH => $length,
                                  -START             => $start,
                                  -END               => $end,
                                  -STRAND            => $strand,
                                  -ADAPTOR           => $self);
352 353 354 355
}



356

357
=head2 fetch_by_name
358

Graham McVicker's avatar
Graham McVicker committed
359
  Arg [1]    : string $name
360 361 362 363 364 365 366 367 368
  Example    : $name  = 'chromosome:NCBI34:X:1000000:2000000:1';
               $slice = $slice_adaptor->fetch_by_name($name);
               $slice2 = $slice_adaptor->fetch_by_name($slice3->name());
  Description: Fetches a slice using a slice name (i.e. the value returned by
               the Slice::name method).  This is useful if you wish to 
               store a unique identifier for a slice in a file or database or
               pass a slice over a network.
               Slice::name allows you to serialise/marshall a slice and this
               method allows you to deserialise/unmarshal it.
Graham McVicker's avatar
Graham McVicker committed
369

370 371 372 373
               Returns undef if no seq_region with the provided name exists in
               the database.

  Returntype : Bio::EnsEMBL::Slice or undef
374 375
  Exceptions : throw if incorrent arg provided
  Caller     : Pipeline
376
  Status     : Stable
377 378 379

=cut

380 381 382
sub fetch_by_name {
  my $self = shift;
  my $name = shift;
Graham McVicker's avatar
Graham McVicker committed
383

384 385
  if(!$name) {
    throw("name argument is required");
Graham McVicker's avatar
Graham McVicker committed
386
  }
387 388 389

  my @array = split(/:/,$name);

390
  if(scalar(@array) < 3 || scalar(@array) > 6) {
391
    throw("Malformed slice name [$name].  Format is " .
Laura Clarke's avatar
 
Laura Clarke committed
392
        "coord_system:version:name:start:end:strand");
393 394
  }

395
  # Rearrange arguments to suit fetch_by_region
396

397 398 399 400 401 402 403 404 405
  my @targetarray;

  $targetarray[0]=$array[0];
  $targetarray[5]=(($array[1]&&$array[1] ne "")?$array[1]:undef);
  $targetarray[1]=(($array[2]&&$array[2] ne "")?$array[2]:undef);
  $targetarray[2]=(($array[3]&&$array[3] ne "")?$array[3]:undef);
  $targetarray[3]=(($array[4]&&$array[4] ne "")?$array[4]:undef);
  $targetarray[4]=(($array[5]&&$array[5] ne "")?$array[5]:undef);
  return $self->fetch_by_region(@targetarray);
Graham McVicker's avatar
Graham McVicker committed
406
}
Graham McVicker's avatar
Graham McVicker committed
407 408 409



410 411 412 413 414
=head2 fetch_by_seq_region_id

  Arg [1]    : string $seq_region_id
               The internal identifier of the seq_region to create this slice
               on
415 416 417
  Arg [2]    : optional start
  Arg [3]    : optional end
  Arg [4]    : optional strand
418 419 420
  Example    : $slice = $slice_adaptor->fetch_by_seq_region_id(34413);
  Description: Creates a slice object of an entire seq_region using the
               seq_region internal identifier to resolve the seq_region.
421 422
               Returns undef if no such slice exists.
  Returntype : Bio::EnsEMBL::Slice or undef
Graham McVicker's avatar
Graham McVicker committed
423 424
  Exceptions : none
  Caller     : general
425
  Status     : Stable
Graham McVicker's avatar
Graham McVicker committed
426 427 428

=cut

429
sub fetch_by_seq_region_id {
430
  my ($self, $seq_region_id,$start,$end,$strand) = @_;
431

432
  my $arr = $self->{'sr_id_cache'}->{ $seq_region_id };
433 434
  my ($name, $length, $cs);

435 436 437 438
  if( $arr ) {
    my $cs_id;
    ($name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
439 440 441 442 443
  } else {
    my $sth = $self->prepare("SELECT name, length, coord_system_id " .
                             "FROM seq_region " .
                             "WHERE seq_region_id = ?");

444 445
    $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
    $sth->execute();
446

447
    return undef if($sth->rows() == 0);
448 449 450 451 452 453 454 455

    my $cs_id;
    ($name, $length, $cs_id) = $sth->fetchrow_array();
    $sth->finish();

    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);

    #cache results to speed up repeated queries
456
    my $arr = [ $seq_region_id, $name, $cs_id, $length ];
457 458 459

    $self->{'sr_name_cache'}->{"$name:$cs_id"} = $arr;
    $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;
460 461
  }

462 463 464
  return Bio::EnsEMBL::Slice->new(-COORD_SYSTEM      => $cs,
                                  -SEQ_REGION_NAME   => $name,
                                  -SEQ_REGION_LENGTH => $length,
465 466 467
                                  -START             => $start || 1,
                                  -END               => $end || $length,
                                  -STRAND            => $strand || 1,
468
                                  -ADAPTOR           => $self);
Arne Stabenau's avatar
Arne Stabenau committed
469 470
}

Graham McVicker's avatar
Graham McVicker committed
471

472 473

=head2 get_seq_region_id
Graham McVicker's avatar
Graham McVicker committed
474

Arne Stabenau's avatar
Arne Stabenau committed
475
  Arg [1]    : Bio::EnsEMBL::Slice $slice
476 477 478 479 480 481 482 483 484 485
               The slice to fetch a seq_region_id for
  Example    : $srid = $slice_adaptor->get_seq_region_id($slice);
  Description: Retrieves the seq_region id (in this database) given a slice
               Seq region ids are not stored on the slices themselves
               because they are intended to be somewhat database independant
               and seq_region_ids vary accross databases.
  Returntype : int
  Exceptions : throw if the seq_region of the slice is not in the db
               throw if incorrect arg provided
  Caller     : BaseFeatureAdaptor
486
  Status     : Stable
Arne Stabenau's avatar
Arne Stabenau committed
487 488

=cut
Graham McVicker's avatar
Graham McVicker committed
489

490 491 492
sub get_seq_region_id {
  my $self = shift;
  my $slice = shift;
Graham McVicker's avatar
Graham McVicker committed
493

494 495 496
  if(!$slice || !ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
    throw('Slice argument is required');
  }
497
  
498
  my $seq_region_name = $slice->seq_region_name();
499
  my $key = $seq_region_name.":".$slice->coord_system->dbID();
500
  my $arr = $self->{'sr_name_cache'}->{"$key"};
501

502 503
  if( $arr ) {
    return $arr->[0];
504 505
  }

506
  my $cs_id = $slice->coord_system->dbID();
507 508 509 510 511 512

  my $sth = $self->prepare("SELECT seq_region_id, length " .
                           "FROM seq_region " .
                           "WHERE name = ? AND coord_system_id = ?");

  #force seq_region_name cast to string so mysql cannot treat as int
513 514 515
  $sth->bind_param(1,"$seq_region_name",SQL_VARCHAR);
  $sth->bind_param(2,$cs_id,SQL_INTEGER);
  $sth->execute();
516 517 518

  if($sth->rows() != 1) {
    throw("Non existant or ambigous seq_region:\n" .
519 520 521
          "  coord_system=[$cs_id],\n" .
          "  name=[$seq_region_name],\n");

522 523 524 525 526 527
  }

  my($seq_region_id, $length) = $sth->fetchrow_array();
  $sth->finish();

  #cache information for future requests
528
  $arr = [ $seq_region_id, $seq_region_name, $cs_id, $length ];
529 530 531 532

  $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
  $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;

533
  return $seq_region_id;
Arne Stabenau's avatar
Arne Stabenau committed
534
}
535 536


Arne Stabenau's avatar
Arne Stabenau committed
537

538 539 540 541 542 543 544 545 546
=head2 fetch_all

  Arg [1]    : string $coord_system_name
               The name of the coordinate system to retrieve slices of.
               This may be a name of an acutal coordinate system or an alias
               to a coordinate system.  Valid aliases are 'seqlevel' or
               'toplevel'.
  Arg [2]    : string $coord_system_version (optional)
               The version of the coordinate system to retrieve slices of
547
  Arg [3]    : bool $include_non_reference (optional)
548 549 550
               If this argument is not provided then only reference slices
               will be returned. If set, both reference and non refeference
               slices will be rerurned.
Graham McVicker's avatar
Graham McVicker committed
551 552
  Arg [4]    : int $include_duplicates (optional)
               If set duplicate regions will be returned.
553 554 555 556 557
               
               NOTE: if you don't use this option and you have a PAR
               (pseudo-autosomal region) at the beginning of your seq_region
               then your slice will not start at position 1, so coordinates
               retrieved from this slice might not be what you expected.
558

559 560 561
  Example    : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
               @contigs = @{$slice_adaptor->fetch_all('contig')};

Graham McVicker's avatar
Graham McVicker committed
562 563 564 565 566
               # get even non-reference regions
               @slices = @{$slice_adaptor->fetch_all('toplevel',undef,1)};

               # include duplicate regions (such as pseudo autosomal regions)
               @slices = @{$slice_adaptor->fetch_all('toplevel', undef,0,1)};
567 568 569 570 571 572

  Description: Retrieves slices of all seq_regions for a given coordinate
               system.  This is analagous to the methods fetch_all which were
               formerly on the ChromosomeAdaptor, RawContigAdaptor and
               CloneAdaptor classes.  Slices fetched span the entire
               seq_regions and are on the forward strand.
573 574
               If the coordinate system with the provided name and version
               does not exist an empty list is returned.
575
               If the coordinate system name provided is 'toplevel', all
576
               non-redundant toplevel slices are returned.
577 578 579 580

               Retrieved slices can be broken into smaller slices using the
               Bio::EnsEMBL::Utils::Slice module.

581
  Returntype : listref of Bio::EnsEMBL::Slices
582
  Exceptions : none
583
  Caller     : general
584
  Status     : Stable
Web Admin's avatar
Web Admin committed
585 586 587

=cut

588 589 590 591 592
sub fetch_all {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift || '';

593
  my ($include_non_reference, $include_duplicates) = @_;
Web Admin's avatar
Web Admin committed
594

595 596 597
  #
  # verify existance of requested coord system and get its id
  #
598 599 600 601 602 603
  my $csa       = $self->db->get_CoordSystemAdaptor();
  my $orig_cs   = $csa->fetch_by_name($cs_name, $cs_version);

  return [] if(!$orig_cs);

  my $sth;
604

605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623
  my %bad_vals=();
  #
  # Get a hash of non reference seq regions
  #
  if(!$include_non_reference){
    my $sth2 = $self->prepare(
			      "SELECT sr.seq_region_id ".
			      "FROM seq_region sr, seq_region_attrib sra, attrib_type at ".
			      " WHERE at.code='non_ref'".
			      "  AND sra.seq_region_id=sr.seq_region_id ".
			      "  AND at.attrib_type_id=sra.attrib_type_id " );
    $sth2->execute();
    my ($seq_region_id);
    $sth2->bind_columns(\$seq_region_id);
    while($sth2->fetch()) {
      $bad_vals{$seq_region_id} = 1;
    }
    $sth2->finish();
  }
624
  #
625
  # Retrieve the seq_regions from the database
626
  #
627
  if($orig_cs->is_top_level()) {
628 629 630 631 632 633 634 635
   $sth =
       $self->prepare("SELECT sr.seq_region_id, sr.name, sr.length, " .
                      "       sr.coord_system_id " .
                      "FROM seq_region sr, " .
                      "     seq_region_attrib sra, attrib_type at " .
                      "WHERE at.code='toplevel' " .
                      "AND   at.attrib_type_id=sra.attrib_type_id " .
                      "AND   sra.seq_region_id=sr.seq_region_id");
636 637
    $sth->execute();
  } else {
638 639 640 641
     $sth =
       $self->prepare('SELECT seq_region_id, name, length, coord_system_id ' .
                      'FROM   seq_region ' .
                      'WHERE  coord_system_id =?');
642 643
     $sth->bind_param(1,$orig_cs->dbID,SQL_INTEGER);
     $sth->execute();
644
  }
645

646 647
  my ($seq_region_id, $name, $length, $cs_id);
  $sth->bind_columns(\$seq_region_id, \$name, \$length, \$cs_id);
648

649
  my $cache_count = 0;
650 651 652

  my @out;
  while($sth->fetch()) {
653 654
    if(!defined($bad_vals{$seq_region_id})){
      my $cs = $csa->fetch_by_dbID($cs_id);
655

656
      if(!$cs) {
657
        throw("seq_region $name references non-existent coord_system $cs_id.");
658
      }
659

660 661
      #cache values for future reference, but stop adding to the cache once we
      #we know we have filled it up
662
      if($cache_count < $Bio::EnsEMBL::Utils::SeqRegionCache::SEQ_REGION_CACHE_SIZE) {
663
        my $arr = [ $seq_region_id, $name, $cs_id, $length ];
664 665 666

        $self->{'sr_name_cache'}->{"$name:$cs_id"} = $arr;
        $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;
667

668
        $cache_count++;
669
      }
670 671 672 673 674 675 676 677 678 679 680

      my $slice = Bio::EnsEMBL::Slice->new
        (-START             => 1,
         -END               => $length,
         -STRAND            => 1,
         -SEQ_REGION_NAME   => $name,
         -SEQ_REGION_LENGTH => $length,
         -COORD_SYSTEM      => $cs,
         -ADAPTOR           => $self);

      if(!defined($include_duplicates) or !$include_duplicates){
681 682 683 684 685 686 687 688 689 690 691 692
        # test if this slice *could* have a duplicate (exception) region
        $self->_build_exception_cache() if(!exists $self->{'asm_exc_cache'});
        if(exists $self->{asm_exc_cache}->{$seq_region_id}) {

          # Dereference symlinked assembly regions.  Take out
          # any regions which are symlinked because these are duplicates
          my @projection = @{$self->fetch_normalized_slice_projection($slice)};
          foreach my $segment ( @projection) {
            if($segment->[2]->seq_region_name() eq $slice->seq_region_name() &&
               $segment->[2]->coord_system->equals($slice->coord_system)) {
              push @out, $segment->[2];
            }
693
          }
694 695 696
        } else {
          # no duplicate regions
          push @out, $slice;
697
        }
698 699
      } else {
        # we want duplicates anyway so do not do any checks
700
        push @out, $slice;
701
      }
702
    }
703
  }
704
  $sth->finish();
705

706
  return \@out;
Web Admin's avatar
Web Admin committed
707 708 709
}


710

Web Admin's avatar
Web Admin committed
711 712 713 714 715 716
=head2 fetch_by_band

 Title   : fetch_by_band
 Usage   :
 Function: create a Slice representing a series of bands
 Example :
717
 Returns : Bio::EnsEMBL::Slice
Web Admin's avatar
Web Admin committed
718
 Args    : the band name
719
 Status     : Stable
Web Admin's avatar
Web Admin committed
720 721 722 723 724 725 726 727 728 729 730

=cut

sub fetch_by_band {
  my ($self,$band) = @_;

  my $sth = $self->db->prepare
        ("select s.name,max(k.seq_region_id)-min(k.seq_region_id, min(k.seq_region_start), max(k.seq_region_id) " .
         "from karyotype as k " .
         "where k.band like ? and k.seq_region_id = s.seq_region_id");

731 732
  $sth->bind_param(1,"$band%",SQL_VARCHAR);
  $sth->execute();
Web Admin's avatar
Web Admin committed
733 734 735 736 737 738 739 740 741 742
  my ( $seq_region_name, $discrepancy, $seq_region_start, $seq_region_end) = $sth->fetchrow_array;

  if($seq_region_name && $discrepancy>0) {
    throw("Band maps to multiple seq_regions");
  } else {
    return $self->fetch_by_region('toplevel',$seq_region_name,$seq_region_start,$seq_region_end);
  }
  throw("Band not recognised in database");
}

743 744 745 746 747 748
=head2 fetch_by_chr_band

 Title   : fetch_by_chr_band
 Usage   :
 Function: create a Slice representing a series of bands
 Example :
749
 Returns : Bio::EnsEMBL::Slice
750
 Args    : the band name
751
 Status     : Stable
752 753 754 755 756 757

=cut

sub fetch_by_chr_band {
  my ($self,$chr,$band) = @_;

Web Admin's avatar
Web Admin committed
758
  my $chr_slice = $self->fetch_by_region('toplevel', $chr);
759 760 761
  my $seq_region_id = $self->get_seq_region_id($chr_slice);

  my $sth = $self->db->prepare
Web Admin's avatar
Web Admin committed
762
        ("select min(k.seq_region_start), max(k.seq_region_end) " .
763 764 765
         "from karyotype as k " .
         "where k.seq_region_id = ? and k.band like ?");

766 767 768
  $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
  $sth->bind_param(2,"$band%",SQL_VARCHAR);
  $sth->execute();
769 770 771
  my ( $slice_start, $slice_end) = $sth->fetchrow_array;

  if(defined $slice_start) {
Web Admin's avatar
Web Admin committed
772
    return $self->fetch_by_region('toplevel',$chr,$slice_start,$slice_end);
773 774 775
  }

  throw("Band not recognised in database");
776 777 778 779
}



Web Admin's avatar
Web Admin committed
780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795
=head2 fetch_by_exon_stable_id

  Arg [1]    : string $exonid
               The stable id of the exon around which the slice is 
               desired
  Arg [2]    : (optional) int $size
               The length of the flanking regions the slice should encompass 
               on either side of the exon (0 by default)
  Example    : $slc = $sa->fetch_by_exon_stable_id('ENSE00000302930',10);
  Description: Creates a slice around the region of the specified exon. 
               If a context size is given, the slice is extended by that 
               number of basepairs on either side of the
               transcript.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : Thrown if the exon is not in the database.
  Caller     : general
796
  Status     : Stable
Web Admin's avatar
Web Admin committed
797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812

=cut

sub fetch_by_exon_stable_id{
  my ($self,$exonid,$size) = @_;

  throw('Exon argument is required.') if(!$exonid);

  my $ea = $self->db->get_ExonAdaptor;
  my $exon = $ea->fetch_by_stable_id($exonid);

  throw("Exon [$exonid] does not exist in DB.") if(!$exon);

  return $self->fetch_by_Feature($exon, $size);
}

Graham McVicker's avatar
Graham McVicker committed
813
=head2 fetch_by_transcript_stable_id
814

Graham McVicker's avatar
Graham McVicker committed
815 816 817 818 819 820 821 822 823
  Arg [1]    : string $transcriptid
               The stable id of the transcript around which the slice is 
               desired
  Arg [2]    : (optional) int $size
               The length of the flanking regions the slice should encompass 
               on either side of the transcript (0 by default)
  Example    : $slc = $sa->fetch_by_transcript_stable_id('ENST00000302930',10);
  Description: Creates a slice around the region of the specified transcript. 
               If a context size is given, the slice is extended by that 
824 825
               number of basepairs on either side of the
               transcript.
Graham McVicker's avatar
Graham McVicker committed
826
  Returntype : Bio::EnsEMBL::Slice
827
  Exceptions : Thrown if the transcript is not in the database.
Graham McVicker's avatar
Graham McVicker committed
828
  Caller     : general
829
  Status     : Stable
830 831 832

=cut

Graham McVicker's avatar
Graham McVicker committed
833
sub fetch_by_transcript_stable_id{
834 835
  my ($self,$transcriptid,$size) = @_;

836 837
  throw('Transcript argument is required.') if(!$transcriptid);

838
  my $ta = $self->db->get_TranscriptAdaptor;
839
  my $transcript = $ta->fetch_by_stable_id($transcriptid);
840

841 842 843 844
  throw("Transcript [$transcriptid] does not exist in DB.") if(!$transcript);

  return $self->fetch_by_Feature($transcript, $size);
}
845

Graham McVicker's avatar
Graham McVicker committed
846 847


Graham McVicker's avatar
Graham McVicker committed
848 849
=head2 fetch_by_transcript_id

Graham McVicker's avatar
Graham McVicker committed
850 851 852 853 854 855 856
  Arg [1]    : int $transcriptid
               The unique database identifier of the transcript around which 
               the slice is desired
  Arg [2]    : (optional) int $size
               The length of the flanking regions the slice should encompass 
               on either side of the transcript (0 by default)
  Example    : $slc = $sa->fetch_by_transcript_id(24, 1000);
857 858 859 860
  Description: Creates a slice around the region of the specified transcript.
               If a context size is given, the slice is extended by that
               number of basepairs on either side of the
               transcript.
Graham McVicker's avatar
Graham McVicker committed
861
  Returntype : Bio::EnsEMBL::Slice
862 863
  Exceptions : throw on incorrect args
               throw if transcript is not in database
Graham McVicker's avatar
Graham McVicker committed
864
  Caller     : general
865
  Status     : Stable
866 867 868

=cut

Graham McVicker's avatar
Graham McVicker committed
869
sub fetch_by_transcript_id {
870
  my ($self,$transcriptid,$size) = @_;
Graham McVicker's avatar
Graham McVicker committed
871

872
  throw('Transcript id argument is required.') if(!$transcriptid);
Graham McVicker's avatar
Graham McVicker committed
873

874 875 876 877 878 879
  my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
  my $transcript = $transcript_adaptor->fetch_by_dbID($transcriptid);

  throw("Transcript [$transcriptid] does not exist in DB.") if(!$transcript);

  return $self->fetch_by_Feature($transcript, $size);
880 881
}

882 883


Graham McVicker's avatar
Graham McVicker committed
884
=head2 fetch_by_gene_stable_id
885

Graham McVicker's avatar
Graham McVicker committed
886
  Arg [1]    : string $geneid
887
               The stable id of the gene around which the slice is
Graham McVicker's avatar
Graham McVicker committed
888 889
               desired
  Arg [2]    : (optional) int $size
Graham McVicker's avatar
Graham McVicker committed
890
               The length of the flanking regions the slice should encompass