SliceAdaptor.pm 65.7 KB
Newer Older
1
=head1 LICENSE
2

3
  Copyright (c) 1999-2011 The European Bioinformatics Institute and
4
  Genome Research Limited.  All rights reserved.
5

6 7 8 9 10 11 12 13
  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
14
  developers list at <dev@ensembl.org>.
15 16 17 18 19

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut
20 21 22

=head1 NAME

23 24
Bio::EnsEMBL::DBSQL::SliceAdaptor - A database aware adaptor responsible for
the creation of Slice objects.
25 26 27

=head1 SYNOPSIS

Graham McVicker's avatar
Graham McVicker committed
28
  use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
29 30 31
  use Bio::EnsEMBL::Registry;

  Bio::EnsEMBL::Registry->load_registry_from_db(
32 33
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
34 35
  );

36 37
  $slice_adaptor =
    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
38

Graham McVicker's avatar
Graham McVicker committed
39
  # get a slice on the entire chromosome X
40
  $chr_slice = $slice_adaptor->fetch_by_region( 'chromosome', 'X' );
Graham McVicker's avatar
Graham McVicker committed
41 42

  # get a slice for each clone in the database
43 44
  foreach $cln_slice ( @{ $slice_adaptor->fetch_all('clone') } ) {
    # do something with clone
45 46
  }

Graham McVicker's avatar
Graham McVicker committed
47
  # get a slice which is part of NT_004321
48 49 50
  $spctg_slice =
    $slice_adaptor->fetch_by_region( 'supercontig', 'NT_004321',
    200_000, 600_000 );
51

52 53
  # get all non-redundant slices from the highest possible coordinate
  # systems
Graham McVicker's avatar
Graham McVicker committed
54 55 56
  $slices = $slice_adaptor->fetch_all('toplevel');

  # include non-reference regions
57
  $slices = $slice_adaptor->fetch_all( 'toplevel', undef, 1 );
Graham McVicker's avatar
Graham McVicker committed
58 59

  # include non-duplicate regions
60
  $slices = $slice_adaptor->fetch_all( 'toplevel', undef, 0, 1 );
Graham McVicker's avatar
Graham McVicker committed
61 62

  # split up a list of slices into smaller slices
63
  $overlap    = 1000;
Graham McVicker's avatar
Graham McVicker committed
64
  $max_length = 1e6;
65
  $slices     = split_Slices( $slices, $max_length, $overlap );
Graham McVicker's avatar
Graham McVicker committed
66 67

  # store a list of slice names in a file
68
  open( FILE, ">$filename" ) or die("Could not open file $filename");
Graham McVicker's avatar
Graham McVicker committed
69 70 71 72 73 74
  foreach my $slice (@$slices) {
    print FILE $slice->name(), "\n";
  }
  close FILE;

  # retreive a list of slices from a file
75 76
  open( FILE, $filename ) or die("Could not open file $filename");
  while ( $name = <FILE> ) {
Graham McVicker's avatar
Graham McVicker committed
77 78 79 80 81
    chomp($name);
    $slice = $slice_adaptor->fetch_by_name($name);
    # do something with slice
  }

82 83
=head1 DESCRIPTION

84 85
This module is responsible for fetching Slices representing genomic
regions from a database.  A Details on how slices can be used are in the
86
Bio::EnsEMBL::Slice module.
87

88
=head1 METHODS
89 90 91 92

=cut


93
package Bio::EnsEMBL::DBSQL::SliceAdaptor;
94 95 96
use vars qw(@ISA);
use strict;

97

98 99
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Slice;
100
use Bio::EnsEMBL::CircularSlice;
101
use Bio::EnsEMBL::Mapper;
Ian Longden's avatar
Ian Longden committed
102
use Bio::EnsEMBL::LRGSlice;
103
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
104

105

106
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
107

108 109
sub new {
  my $caller = shift;
110

111
  my $class = ref($caller) || $caller;
112

113
  my $self = $class->SUPER::new(@_);
114

115 116
  # use a cache which is shared and also used by the assembly
  # mapper adaptor
117

118 119 120 121
  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'};
122

Ian Longden's avatar
Ian Longden committed
123 124 125 126

  $self->{'lrg_region_test'} = undef;
  my $meta_container = $self->db->get_MetaContainer();
  my @values = $meta_container->list_value_by_key("LRG");
127
  if(scalar(@values) and $values[0]->[0]){
Ian Longden's avatar
Ian Longden committed
128 129
    $self->{'lrg_region_test'} = $values[0]->[0];
  }
130 131 132 133 134 135
  return $self;
}


=head2 fetch_by_region

136
  Arg [1]    : string $coord_system_name (optional)
137
               The name of the coordinate system of the slice to be created
138
               This may be a name of an actual coordinate system or an alias
139 140 141 142
               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
143
               created on.
144 145 146 147 148 149 150 151
  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)
152 153
  Arg [7]    : boolean $no_fuzz (optional, default = undef (false))
               If true (non-zero), do not use "fuzzy matching" (see below).
154 155 156
  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
157 158 159 160 161 162 163 164 165 166 167
               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.
168 169 170 171 172 173 174

               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'.

175 176 177
               The fuzzy matching can be turned off by setting the
               $no_fuzz argument to a true value.

178 179 180 181 182 183 184
               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
185
  Caller     : general
186
  Status     : Stable
187 188 189

=cut

190 191 192 193

#
# ARNE: This subroutine needs simplification!! 
#
194
sub fetch_by_region {
195 196 197
  my ( $self, $coord_system_name, $seq_region_name, $start, $end,
       $strand, $version, $no_fuzz )
    = @_;
198

199 200
  if ( !defined($start) )  { $start  = 1 }
  if ( !defined($strand) ) { $strand = 1 }
201

202 203 204
  if ( !defined($seq_region_name) ) {
    throw('seq_region_name argument is required');
  }
205

206 207
  my $cs;
  my $csa = $self->db->get_CoordSystemAdaptor();
208

209 210
  if ( defined($coord_system_name) ) {
    $cs = $csa->fetch_by_name( $coord_system_name, $version );
211

212
    ## REMOVE THESE THREE LINES WHEN STICKLEBACK DB IS FIXED!
213 214 215 216 217 218 219
    ## Anne/ap5 (2007-10-09):
    # The problem was that the stickleback genebuild called the
    # chromosomes 'groups', which meant they weren't being picked out by
    # the karyotype drawing code.  Apparently they are usually called
    # 'groups' in the stickleback community, even though they really are
    # chromosomes!

220 221
    if ( !defined($cs) && $coord_system_name eq 'chromosome' ) {
      $cs = $csa->fetch_by_name( 'group', $version );
222 223
    }

224
    if ( !defined($cs) ) {
225
      throw( sprintf( "Unknown coordinate system:\n"
226
                        . "name='%s' version='%s'\n",
227
                      $coord_system_name, $version ) );
228
    }
229

230
    # fetching by toplevel is same as fetching w/o name or version
231 232
    if ( $cs->is_top_level() ) {
      $cs      = undef;
233 234
      $version = undef;
    }
235

236
  } ## end if ( defined($coord_system_name...))
237 238 239

  my $constraint;
  my $sql;
240
  my @bind_params;
241 242
  my $key;

243 244 245 246
  if ( defined($cs) ) {
    $sql = sprintf( "SELECT sr.name, sr.seq_region_id, sr.length, %d "
                      . "FROM seq_region sr ",
                    $cs->dbID() );
247

248 249
    $constraint = "AND sr.coord_system_id = ?";
    push( @bind_params, [ $cs->dbID(), SQL_INTEGER ] );
250

251
    $key = "$seq_region_name:" . $cs->dbID();
252
  } else {
253 254 255
    $sql =
      "SELECT sr.name, sr.seq_region_id, sr.length, cs.coord_system_id "
      . "FROM seq_region sr, coord_system cs ";
256

257 258 259 260 261
    $constraint = "AND sr.coord_system_id = cs.coord_system_id "
      . "AND cs.species_id = ? ";
    push( @bind_params, [ $self->species_id(), SQL_INTEGER ] );

    if ( defined($version) ) {
262
      $constraint .= "AND cs.version = ? ";
263
      push( @bind_params, [ $version, SQL_VARCHAR ] );
264
    }
265

266
    $constraint .= "ORDER BY cs.rank ASC";
267 268
  }

269
  # check the cache so we only go to the db if necessary
270
  my $length;
271
  my $arr;
272

273 274 275
  if ( defined($key) ) { $arr = $self->{'sr_name_cache'}->{$key} }

  if ( defined($arr) ) {
276
    $length = $arr->[3];
277
  } else {
278 279 280 281 282 283 284 285
    my $sth =
      $self->prepare( $sql . "WHERE sr.name = ? " . $constraint );

    unshift( @bind_params, [ $seq_region_name, SQL_VARCHAR ] );

    my $pos = 0;
    foreach my $param (@bind_params) {
      $sth->bind_param( ++$pos, $param->[0], $param->[1] );
286
    }
287 288

    $sth->execute();
289

290
    if ( $sth->rows() == 0 ) {
291
      $sth->finish();
Graham McVicker's avatar
Graham McVicker committed
292

293 294 295 296 297 298 299 300 301 302 303 304 305 306

      # try synonyms
      my $syn_sql_sth = $self->prepare("select s.name from seq_region s, seq_region_synonym ss where s.seq_region_id = ss.seq_region_id and ss.synonym = ?");
      $syn_sql_sth->bind_param(1, $seq_region_name, SQL_VARCHAR);
      $syn_sql_sth->execute();
      my $new_name;
      $syn_sql_sth->bind_columns( \$new_name);
      if($syn_sql_sth->fetch){
	$syn_sql_sth->finish;
	return $self->fetch_by_region($coord_system_name, $new_name, $start, $end, $strand, $version, $no_fuzz);
      }
      $syn_sql_sth->finish;


307 308
      if ($no_fuzz) { return undef }

309 310
      # Do fuzzy matching, assuming that we are just missing a version
      # on the end of the seq_region name.
311

312 313
      $sth =
        $self->prepare( $sql . " WHERE sr.name LIKE ? " . $constraint );
314

315 316 317 318 319 320
      $bind_params[0] =
        [ sprintf( '%s.%%', $seq_region_name ), SQL_VARCHAR ];

      $pos = 0;
      foreach my $param (@bind_params) {
        $sth->bind_param( ++$pos, $param->[0], $param->[1] );
321
      }
322

323
      $sth->execute();
324 325

      my $prefix_len = length($seq_region_name) + 1;
326 327
      my $high_ver   = undef;
      my $high_cs    = $cs;
328

329 330
      # Find the fuzzy-matched seq_region with the highest postfix
      # (which ought to be a version).
331

332 333
      my ( $tmp_name, $id, $tmp_length, $cs_id );
      $sth->bind_columns( \( $tmp_name, $id, $tmp_length, $cs_id ) );
334

Felix Kokocinski's avatar
Felix Kokocinski committed
335
      my $i = 0;
336

337 338 339
      while ( $sth->fetch ) {
        my $tmp_cs =
          ( defined($cs) ? $cs : $csa->fetch_by_dbID($cs_id) );
340

341
        # cache values for future reference
342
        my $arr = [ $id, $tmp_name, $cs_id, $tmp_length ];
343
        $self->{'sr_name_cache'}->{"$tmp_name:$cs_id"} = $arr;
344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362
        $self->{'sr_id_cache'}->{"$id"}                = $arr;

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

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

        # 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
363
        }
364 365

        $i++;
366
      } ## end while ( $sth->fetch )
367 368
      $sth->finish();

369
      # warn if fuzzy matching found more than one result
370 371 372 373 374 375 376
      if ( $i > 1 ) {
        warning(
          sprintf(
            "Fuzzy matching of seq_region_name "
              . "returned more than one result.\n"
              . "You might want to check whether the returned seq_region\n"
              . "(%s:%s) is the one you intended to fetch.\n",
377
            $high_cs->name(), $seq_region_name ) );
378 379
      }

380 381
      $cs = $high_cs;

382 383
      # return if we did not find any appropriate match:
      if ( !defined($high_ver) ) { return undef }
384

385 386
    } else {

387 388 389
      my ( $id, $cs_id );
      ( $seq_region_name, $id, $length, $cs_id ) =
        $sth->fetchrow_array();
390
      $sth->finish();
391

392
      # cache to speed up for future queries
393
      my $arr = [ $id, $seq_region_name, $cs_id, $length ];
394
      $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
395 396
      $self->{'sr_id_cache'}->{"$id"}                       = $arr;
      $cs = $csa->fetch_by_dbID($cs_id);
397
    }
398
  } ## end else [ if ( defined($arr) ) ]
399

400
  if ( !defined($end) ) { $end = $length }
Graham McVicker's avatar
Graham McVicker committed
401

402
  if ( $end + 1 < $start ) {
403 404 405 406 407 408 409 410 411 412 413
    my $new_sl =
      Bio::EnsEMBL::CircularSlice->new(
                                   -COORD_SYSTEM    => $cs,
                                   -SEQ_REGION_NAME => $seq_region_name,
                                   -SEQ_REGION_LENGTH => $length,
                                   -START             => $start,
                                   -END               => $end,
                                   -STRAND            => 1,
                                   -ADAPTOR           => $self );

    return $new_sl;
414 415
  }

416 417 418
  if ( defined( $self->{'lrg_region_test'} )
       and substr( $cs->name, 0, 3 ) eq $self->{'lrg_region_test'} )
  {
Ian Longden's avatar
Ian Longden committed
419
    return
420 421 422 423 424 425 426 427
      Bio::EnsEMBL::LRGSlice->new( -COORD_SYSTEM    => $cs,
                                   -SEQ_REGION_NAME => $seq_region_name,
                                   -SEQ_REGION_LENGTH => $length,
                                   -START             => $start,
                                   -END               => $end,
                                   -STRAND            => $strand,
                                   -ADAPTOR           => $self );
  } else {
Ian Longden's avatar
Ian Longden committed
428
    return
429 430 431 432 433 434 435 436
      Bio::EnsEMBL::Slice->new_fast( {
                                  'coord_system'    => $cs,
                                  'seq_region_name' => $seq_region_name,
                                  'seq_region_length' => $length,
                                  'start'             => $start,
                                  'end'               => $end,
                                  'strand'            => $strand,
                                  'adaptor'           => $self } );
Ian Longden's avatar
Ian Longden committed
437
  }
438
} ## end sub fetch_by_region
439

440
=head2 fetch_by_region_unique
441

442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463
  Arg [1]    : string $coord_system_name (optional)
               The name of the coordinate system of the slice to be created
               This may be a name of an actual coordinate system or an alias
               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
               created on.
  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)
  Arg [7]    : boolean $no_fuzz (optional, default = undef (false))
               If true (non-zero), do not use "fuzzy matching" (see below).
  Example    : $slice = $slice_adaptor->fetch_by_region_unique('chromosome', 'HSCHR6_MHC_COX');
  Description: Retrieves a slice on the requested region but returns only the unique
               parts of the slice.  At a minimum the
               name the name of the seq_region to fetch must be provided.
464

465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498
               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.

               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'.

               The fuzzy matching can be turned off by setting the
               $no_fuzz argument to a true value.

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

  Returntype : listref Bio::EnsEMBL::Slice
  Exceptions : throw if no seq_region_name is provided
               throw if invalid coord_system_name is provided
               throw if start > end is provided
  Caller     : general
  Status     : Stable

=cut

sub fetch_by_region_unique {
  my $self = shift;

499
  my @out   = ();
500
  my $slice = $self->fetch_by_region(@_);
501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519

  if ( !exists( $self->{'asm_exc_cache'} ) ) {
    $self->_build_exception_cache();
  }

  if ( exists(
          $self->{'asm_exc_cache'}->{ $self->get_seq_region_id($slice) }
       ) )
  {
    # 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] );
520 521 522
      }
    }
  }
523

524
  return \@out;
525
} ## end sub fetch_by_region_unique
526

527
=head2 fetch_by_name
528

Graham McVicker's avatar
Graham McVicker committed
529
  Arg [1]    : string $name
530 531 532 533 534 535 536 537 538
  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
539

540 541 542 543
               Returns undef if no seq_region with the provided name exists in
               the database.

  Returntype : Bio::EnsEMBL::Slice or undef
544 545
  Exceptions : throw if incorrent arg provided
  Caller     : Pipeline
546
  Status     : Stable
547 548 549

=cut

550 551 552
sub fetch_by_name {
  my $self = shift;
  my $name = shift;
Graham McVicker's avatar
Graham McVicker committed
553

554 555
  if(!$name) {
    throw("name argument is required");
Graham McVicker's avatar
Graham McVicker committed
556
  }
557 558 559

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

560
  if(scalar(@array) < 3 || scalar(@array) > 6) {
561
    throw("Malformed slice name [$name].  Format is " .
Laura Clarke's avatar
 
Laura Clarke committed
562
        "coord_system:version:name:start:end:strand");
563 564
  }

565
  # Rearrange arguments to suit fetch_by_region
566

567 568 569 570 571 572 573 574 575
  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
576
}
Graham McVicker's avatar
Graham McVicker committed
577 578 579



580 581 582 583 584
=head2 fetch_by_seq_region_id

  Arg [1]    : string $seq_region_id
               The internal identifier of the seq_region to create this slice
               on
585 586 587
  Arg [2]    : optional start
  Arg [3]    : optional end
  Arg [4]    : optional strand
588 589 590
  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.
591 592
               Returns undef if no such slice exists.
  Returntype : Bio::EnsEMBL::Slice or undef
Graham McVicker's avatar
Graham McVicker committed
593 594
  Exceptions : none
  Caller     : general
595
  Status     : Stable
Graham McVicker's avatar
Graham McVicker committed
596 597 598

=cut

599
sub fetch_by_seq_region_id {
600
  my ( $self, $seq_region_id, $start, $end, $strand ) = @_;
601

602 603
  my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
  my ( $name, $length, $cs, $cs_id );
604

605 606
  if ( $arr && defined( $arr->[2] ) ) {
    ( $name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
607
    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
608
  } else {
609 610
    my $sth =
      $self->prepare(   "SELECT sr.name, sr.coord_system_id, sr.length "
611
                      . "FROM seq_region sr "
612
                      . "WHERE sr.seq_region_id = ? " );
613

614
    $sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
615
    $sth->execute();
616

617
    if ( $sth->rows() == 0 ) { return undef }
618

619
    ( $name, $cs_id, $length ) = $sth->fetchrow_array();
620 621 622 623 624
    $sth->finish();

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

    #cache results to speed up repeated queries
625
    my $arr = [ $seq_region_id, $name, $cs_id, $length ];
626 627 628

    $self->{'sr_name_cache'}->{"$name:$cs_id"} = $arr;
    $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;
629 630
  }

631
  return
632 633 634 635 636 637 638 639
    Bio::EnsEMBL::Slice->new_fast({ 
	                      'coord_system'     => $cs,
                              'seq_region_name'  => $name,
                              'seq_region_length'=> $length,
                              'start'            => $start || 1,
                              'end'              => $end || $length,
                              'strand'           => $strand || 1,
                              'adaptor'           => $self} );
640
} ## end sub fetch_by_seq_region_id
Arne Stabenau's avatar
Arne Stabenau committed
641

Graham McVicker's avatar
Graham McVicker committed
642

643 644

=head2 get_seq_region_id
Graham McVicker's avatar
Graham McVicker committed
645

Arne Stabenau's avatar
Arne Stabenau committed
646
  Arg [1]    : Bio::EnsEMBL::Slice $slice
647 648 649 650 651 652 653 654 655 656
               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
657
  Status     : Stable
Arne Stabenau's avatar
Arne Stabenau committed
658 659

=cut
Graham McVicker's avatar
Graham McVicker committed
660

661 662 663
sub get_seq_region_id {
  my $self = shift;
  my $slice = shift;
Graham McVicker's avatar
Graham McVicker committed
664

Ian Longden's avatar
Ian Longden committed
665
  if(!$slice || !ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
666 667
    throw('Slice argument is required');
  }
668
  
669
  my $seq_region_name = $slice->seq_region_name();
670
  my $key = $seq_region_name.":".$slice->coord_system->dbID();
671
  my $arr = $self->{'sr_name_cache'}->{"$key"};
672

673 674
  if( $arr ) {
    return $arr->[0];
675 676
  }

677
  my $cs_id = $slice->coord_system->dbID();
678 679 680 681 682 683

  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
684 685 686
  $sth->bind_param(1,"$seq_region_name",SQL_VARCHAR);
  $sth->bind_param(2,$cs_id,SQL_INTEGER);
  $sth->execute();
687 688 689

  if($sth->rows() != 1) {
    throw("Non existant or ambigous seq_region:\n" .
690 691 692
          "  coord_system=[$cs_id],\n" .
          "  name=[$seq_region_name],\n");

693 694 695 696 697 698
  }

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

  #cache information for future requests
699
  $arr = [ $seq_region_id, $seq_region_name, $cs_id, $length ];
700 701 702 703

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

704
  return $seq_region_id;
Arne Stabenau's avatar
Arne Stabenau committed
705
}
706 707


Arne Stabenau's avatar
Arne Stabenau committed
708

709 710 711 712 713 714 715 716 717
=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
718
  Arg [3]    : bool $include_non_reference (optional)
719 720 721
               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
722 723
  Arg [4]    : int $include_duplicates (optional)
               If set duplicate regions will be returned.
724
               
725
               NOTE: if you do not use this option and you have a PAR
726 727 728
               (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.
729

730 731 732 733
  Arg[5]     : bool $include_lrg (optional)  (default 0)
               If set lrg regions will be returned aswell.


734 735 736
  Example    : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
               @contigs = @{$slice_adaptor->fetch_all('contig')};

Graham McVicker's avatar
Graham McVicker committed
737 738 739 740 741
               # 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)};
742 743 744 745 746 747

  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.
748 749
               If the coordinate system with the provided name and version
               does not exist an empty list is returned.
750
               If the coordinate system name provided is 'toplevel', all
751 752
               non-redundant toplevel slices are returned (note that any
               coord_system_version argument is ignored in that case).
753 754 755 756

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

757
  Returntype : listref of Bio::EnsEMBL::Slices
758
  Exceptions : none
759
  Caller     : general
760
  Status     : Stable
Web Admin's avatar
Web Admin committed
761 762 763

=cut

764 765 766 767 768
sub fetch_all {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift || '';

769
  my ($include_non_reference, $include_duplicates, $include_lrg) = @_;
Web Admin's avatar
Web Admin committed
770

771 772 773
  #
  # verify existance of requested coord system and get its id
  #
774 775 776
  my $csa       = $self->db->get_CoordSystemAdaptor();
  my $orig_cs   = $csa->fetch_by_name($cs_name, $cs_version);

777
  return [] if ( !$orig_cs );
778

779
  my %bad_vals=();
780

781 782 783
  #
  # Get a hash of non reference seq regions
  #
784
  if ( !$include_non_reference ) {
785
    my $sth =
786 787 788 789 790 791 792 793 794
      $self->prepare(   'SELECT sr.seq_region_id '
                      . 'FROM seq_region sr, seq_region_attrib sra, '
                      . 'attrib_type at, coord_system cs '
                      . 'WHERE at.code = "non_ref" '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

795 796
    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();
797

798
    my ($seq_region_id);
799
    $sth->bind_columns( \$seq_region_id );
800

801
    while ( $sth->fetch() ) {
802 803 804
      $bad_vals{$seq_region_id} = 1;
    }
  }
805

806 807 808
  #
  # if we do not want lrg's then add them to the bad list;
  #
809 810
  if ( !$include_lrg ) {
    my $sth =
811 812 813 814 815 816 817 818 819
      $self->prepare(   'SELECT sr.seq_region_id '
                      . 'FROM seq_region sr, seq_region_attrib sra, '
                      . 'attrib_type at, coord_system cs '
                      . 'WHERE at.code = "LRG" '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

820 821
    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();
822 823

    my ($seq_region_id);
824
    $sth->bind_columns( \$seq_region_id );
825

826
    while ( $sth->fetch() ) {
827 828 829 830
      $bad_vals{$seq_region_id} = 1;
    }
  }

831
  #
832
  # Retrieve the seq_regions from the database
833
  #
834 835

  my $sth;
836 837 838 839 840 841 842 843 844 845 846 847 848
  if ( $orig_cs->is_top_level() ) {
    $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, coord_system cs '
                      . 'WHERE at.code = "toplevel" '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
849 850
    $sth->execute();
  } else {
851
    $sth =
852 853 854 855
      $self->prepare(   'SELECT sr.seq_region_id, sr.name, '
                      . 'sr.length, sr.coord_system_id '
                      . 'FROM seq_region sr '
                      . 'WHERE sr.coord_system_id = ?' );
856 857 858

    $sth->bind_param( 1, $orig_cs->dbID, SQL_INTEGER );
    $sth->execute();
859
  }
860

861 862
  my ( $seq_region_id, $name, $length, $cs_id );
  $sth->bind_columns( \( $seq_region_id, $name, $length, $cs_id ) );
863

864
  my $cache_count = 0;
865 866 867

  my @out;
  while($sth->fetch()) {
868 869
    if(!defined($bad_vals{$seq_region_id})){
      my $cs = $csa->fetch_by_dbID($cs_id);
870

871
      if(!$cs) {
872
        throw("seq_region $name references non-existent coord_system $cs_id.");