SliceAdaptor.pm 69.6 KB
Newer Older
1
=head1 LICENSE
2

Andy Yates's avatar
Andy Yates committed
3
  Copyright (c) 1999-2012 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
  $self->{'lrg_region_test'} = undef;
  my $meta_container = $self->db->get_MetaContainer();
  my @values = $meta_container->list_value_by_key("LRG");
126
  if(scalar(@values) and $values[0]->[0]){
Ian Longden's avatar
Ian Longden committed
127 128
    $self->{'lrg_region_test'} = $values[0]->[0];
  }
129 130 131 132 133 134
  return $self;
}


=head2 fetch_by_region

135
  Arg [1]    : string $coord_system_name (optional)
136
               The name of the coordinate system of the slice to be created
137
               This may be a name of an actual coordinate system or an alias
138 139 140 141
               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
142
               created on.
143 144 145 146 147 148 149 150
  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)
151 152
  Arg [7]    : boolean $no_fuzz (optional, default = undef (false))
               If true (non-zero), do not use "fuzzy matching" (see below).
153 154 155
  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
156 157 158 159 160 161 162 163 164 165 166
               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.
167 168 169 170 171 172 173

               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'.

174 175 176
               The fuzzy matching can be turned off by setting the
               $no_fuzz argument to a true value.

177 178 179 180 181 182 183
               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
184
  Caller     : general
185
  Status     : Stable
186 187 188

=cut

189 190 191 192

#
# ARNE: This subroutine needs simplification!! 
#
193
sub fetch_by_region {
194 195 196
  my ( $self, $coord_system_name, $seq_region_name, $start, $end,
       $strand, $version, $no_fuzz )
    = @_;
197

198 199
  if ( !defined($start) )  { $start  = 1 }
  if ( !defined($strand) ) { $strand = 1 }
200

201 202 203
  if ( !defined($seq_region_name) ) {
    throw('seq_region_name argument is required');
  }
204

205 206
  my $cs;
  my $csa = $self->db->get_CoordSystemAdaptor();
207

208 209
  if ( defined($coord_system_name) ) {
    $cs = $csa->fetch_by_name( $coord_system_name, $version );
210

211
    ## REMOVE THESE THREE LINES WHEN STICKLEBACK DB IS FIXED!
212 213 214 215 216 217 218
    ## 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!

219 220
    if ( !defined($cs) && $coord_system_name eq 'chromosome' ) {
      $cs = $csa->fetch_by_name( 'group', $version );
221 222
    }

223
    if ( !defined($cs) ) {
224
      throw( sprintf( "Unknown coordinate system:\n"
225
                        . "name='%s' version='%s'\n",
226
                      $coord_system_name, $version ) );
227
    }
228

229
    # fetching by toplevel is same as fetching w/o name or version
230 231
    if ( $cs->is_top_level() ) {
      $cs      = undef;
232 233
      $version = undef;
    }
234

235
  } ## end if ( defined($coord_system_name...))
236 237 238

  my $constraint;
  my $sql;
239
  my @bind_params;
240 241
  my $key;

242 243 244 245
  if ( defined($cs) ) {
    $sql = sprintf( "SELECT sr.name, sr.seq_region_id, sr.length, %d "
                      . "FROM seq_region sr ",
                    $cs->dbID() );
246

247 248
    $constraint = "AND sr.coord_system_id = ?";
    push( @bind_params, [ $cs->dbID(), SQL_INTEGER ] );
249

250
    $key = "$seq_region_name:" . $cs->dbID();
251
  } else {
252 253 254
    $sql =
      "SELECT sr.name, sr.seq_region_id, sr.length, cs.coord_system_id "
      . "FROM seq_region sr, coord_system cs ";
255

256 257 258 259 260
    $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) ) {
261
      $constraint .= "AND cs.version = ? ";
262
      push( @bind_params, [ $version, SQL_VARCHAR ] );
263
    }
264

265
    $constraint .= "ORDER BY cs.rank ASC";
266 267
  }

268
  # check the cache so we only go to the db if necessary
269
  my $length;
270
  my $arr;
271

272 273 274
  if ( defined($key) ) { $arr = $self->{'sr_name_cache'}->{$key} }

  if ( defined($arr) ) {
275
    $length = $arr->[3];
276
  } else {
277 278 279 280 281 282 283 284
    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] );
285
    }
286 287

    $sth->execute();
288

289
    if ( $sth->rows() == 0 ) {
290
      $sth->finish();
Graham McVicker's avatar
Graham McVicker committed
291

292 293 294 295 296 297 298 299 300 301 302 303 304 305

      # 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;


306 307
      if ($no_fuzz) { return undef }

308 309
      # Do fuzzy matching, assuming that we are just missing a version
      # on the end of the seq_region name.
310

311 312
      $sth =
        $self->prepare( $sql . " WHERE sr.name LIKE ? " . $constraint );
313

314 315 316 317 318 319
      $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] );
320
      }
321

322
      $sth->execute();
323 324

      my $prefix_len = length($seq_region_name) + 1;
325 326
      my $high_ver   = undef;
      my $high_cs    = $cs;
327

328 329
      # Find the fuzzy-matched seq_region with the highest postfix
      # (which ought to be a version).
330

331 332
      my ( $tmp_name, $id, $tmp_length, $cs_id );
      $sth->bind_columns( \( $tmp_name, $id, $tmp_length, $cs_id ) );
333

Felix Kokocinski's avatar
Felix Kokocinski committed
334
      my $i = 0;
335

336 337 338
      while ( $sth->fetch ) {
        my $tmp_cs =
          ( defined($cs) ? $cs : $csa->fetch_by_dbID($cs_id) );
339

340
        # cache values for future reference
341
        my $arr = [ $id, $tmp_name, $cs_id, $tmp_length ];
342
        $self->{'sr_name_cache'}->{"$tmp_name:$cs_id"} = $arr;
343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361
        $self->{'sr_id_cache'}->{"$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
362
        }
363 364

        $i++;
365
      } ## end while ( $sth->fetch )
366 367
      $sth->finish();

368
      # warn if fuzzy matching found more than one result
369 370 371 372 373 374 375
      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",
376
            $high_cs->name(), $seq_region_name ) );
377 378
      }

379 380
      $cs = $high_cs;

381 382
      # return if we did not find any appropriate match:
      if ( !defined($high_ver) ) { return undef }
383

384 385
    } else {

386 387 388
      my ( $id, $cs_id );
      ( $seq_region_name, $id, $length, $cs_id ) =
        $sth->fetchrow_array();
389
      $sth->finish();
390

391
      # cache to speed up for future queries
392
      my $arr = [ $id, $seq_region_name, $cs_id, $length ];
393
      $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
394 395
      $self->{'sr_id_cache'}->{"$id"}                       = $arr;
      $cs = $csa->fetch_by_dbID($cs_id);
396
    }
397
  } ## end else [ if ( defined($arr) ) ]
398

399
  if ( !defined($end) ) { $end = $length }
Graham McVicker's avatar
Graham McVicker committed
400

401 402
  #If this was given then check if we've got a circular seq region otherwise
  #let it fall through to the normal Slice method
403
  if ( $end + 1 < $start ) {
404 405 406 407 408 409 410 411 412 413 414 415 416 417 418
    my $cs_id = $cs->dbID();
    my $seq_region_id = $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr->[0];
    if($self->is_circular($seq_region_id)) {
      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;
    }
419 420
  }

421 422 423
  if ( defined( $self->{'lrg_region_test'} )
       and substr( $cs->name, 0, 3 ) eq $self->{'lrg_region_test'} )
  {
Ian Longden's avatar
Ian Longden committed
424
    return
425 426 427 428 429 430 431 432
      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
433
    return
434 435 436 437 438 439 440 441
      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
442
  }
443
} ## end sub fetch_by_region
444

445 446 447
=head2 fetch_by_toplevel_location

  Arg [1]     : string $location
448 449 450
                Ensembl formatted location. Can be a format like 
                C<name:start-end>, C<name:start..end>, C<name:start> and
                C<name>.
451 452
  Arg[2]      : boolean $no_warnings
                Suppress warnings from this method
453 454 455 456
  Example     : my $slice = $sa->fetch_by_toplevel_location('X:1-10000')
  Description : Converts an Ensembl location/region into the sequence region
                name, start and end and passes them onto C<fetch_by_region()>. 
                The code assumes that the required slice is on the top level
457 458
                coordinate system. The code assumes that location formatting
                is not perfect and will perform basic cleanup before parsing.
459 460 461 462 463 464 465 466
  Returntype  : Bio::EnsEMBL::Slice
  Exceptions  : If $location is false otherwise see C<fetch_by_region()>
  Caller      : General
  Status      : Beta

=cut

sub fetch_by_toplevel_location {
467
  my ($self, $location, $no_warnings) = @_;
468
  throw 'You must specify a location' if ! $location;
469 470
  
  my $regex = qr/^(\w+) :? (\d+)? (?:-|[.]{2})? (\d+)?$/xms;
471
  my $number_seps_regex = qr/\s+|,|_/;
472 473 474 475 476 477 478 479 480 481 482
  
  if(my ($seq_region_name, $start, $end) = $location =~ $regex) {
    if(defined $start && $start < 1) {
      warning "Start was less than 1 (${start}) which is not allowed. Resetting to 1"  if ! $no_warnings;
      $start = 1;
    }
    if(defined $end && $end < 1) {
      throw "Cannot request negative or 0 end indexes through this interface. Given $end but expected something greater than 0";
    }
    
    my $coord_system_name = 'toplevel';
483 484 485 486 487
    
    #cleanup any nomenclature like 1_000 or 1 000 or 1,000
    $start =~ s/$number_seps_regex//g;
    $end =~ s/$number_seps_regex//g;
    
488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503
    my $slice = $self->fetch_by_region($coord_system_name, $seq_region_name, $start, $end, undef, undef, 0);
    return unless $slice;
    
    my $srl = $slice->seq_region_length();
    my $name = $slice->seq_region_name();
    if(defined $start && $start > $srl) {
      throw "Cannot request a slice whose start ($start) is greater than $srl for $name.";
    }
    if(defined $end && $end > $srl) {
      warning "Requested end ($end) is greater than $srl for $name. Resetting to $srl" if ! $no_warnings;
      $slice->{end} = $srl;
    }
    
    return $slice;
  }
  return;
504 505
}

506
=head2 fetch_by_region_unique
507

508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529
  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.
530

531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564
               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;

565
  my @out   = ();
566
  my $slice = $self->fetch_by_region(@_);
567

568

569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586
  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] );
587 588 589
      }
    }
  }
590

591
  return \@out;
592
} ## end sub fetch_by_region_unique
593

594
=head2 fetch_by_name
595

Graham McVicker's avatar
Graham McVicker committed
596
  Arg [1]    : string $name
597 598 599 600 601 602 603 604 605
  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
606

607 608 609 610
               Returns undef if no seq_region with the provided name exists in
               the database.

  Returntype : Bio::EnsEMBL::Slice or undef
611 612
  Exceptions : throw if incorrent arg provided
  Caller     : Pipeline
613
  Status     : Stable
614 615 616

=cut

617 618 619
sub fetch_by_name {
  my $self = shift;
  my $name = shift;
Graham McVicker's avatar
Graham McVicker committed
620

621 622
  if(!$name) {
    throw("name argument is required");
Graham McVicker's avatar
Graham McVicker committed
623
  }
624 625 626

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

627
  if(scalar(@array) < 3 || scalar(@array) > 6) {
628
    throw("Malformed slice name [$name].  Format is " .
Laura Clarke's avatar
 
Laura Clarke committed
629
        "coord_system:version:name:start:end:strand");
630 631
  }

632
  # Rearrange arguments to suit fetch_by_region
633

634 635 636 637 638 639 640 641 642
  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
643
}
Graham McVicker's avatar
Graham McVicker committed
644 645 646



647 648 649 650 651
=head2 fetch_by_seq_region_id

  Arg [1]    : string $seq_region_id
               The internal identifier of the seq_region to create this slice
               on
652 653 654
  Arg [2]    : optional start
  Arg [3]    : optional end
  Arg [4]    : optional strand
655 656 657
  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.
658 659
               Returns undef if no such slice exists.
  Returntype : Bio::EnsEMBL::Slice or undef
Graham McVicker's avatar
Graham McVicker committed
660 661
  Exceptions : none
  Caller     : general
662
  Status     : Stable
Graham McVicker's avatar
Graham McVicker committed
663 664 665

=cut

666
sub fetch_by_seq_region_id {
667
  my ( $self, $seq_region_id, $start, $end, $strand ) = @_;
668

669 670
  my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
  my ( $name, $length, $cs, $cs_id );
671

672

673 674
  if ( $arr && defined( $arr->[2] ) ) {
    ( $name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
675
    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
676
  } else {
677 678
    my $sth =
      $self->prepare(   "SELECT sr.name, sr.coord_system_id, sr.length "
679
                      . "FROM seq_region sr "
680
                      . "WHERE sr.seq_region_id = ? " );
681

682
    $sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
683
    $sth->execute();
684

685
    if ( $sth->rows() == 0 ) { return undef }
686

687
    ( $name, $cs_id, $length ) = $sth->fetchrow_array();
688 689 690 691 692
    $sth->finish();

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

    #cache results to speed up repeated queries
693
    my $arr = [ $seq_region_id, $name, $cs_id, $length ];
694 695 696

    $self->{'sr_name_cache'}->{"$name:$cs_id"} = $arr;
    $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;
697 698
  }

699
  return
700 701 702 703 704 705 706 707
    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} );
708
} ## end sub fetch_by_seq_region_id
Arne Stabenau's avatar
Arne Stabenau committed
709

Graham McVicker's avatar
Graham McVicker committed
710

711 712

=head2 get_seq_region_id
Graham McVicker's avatar
Graham McVicker committed
713

Arne Stabenau's avatar
Arne Stabenau committed
714
  Arg [1]    : Bio::EnsEMBL::Slice $slice
715 716 717 718 719 720 721 722 723 724
               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
725
  Status     : Stable
Arne Stabenau's avatar
Arne Stabenau committed
726 727

=cut
Graham McVicker's avatar
Graham McVicker committed
728

729 730 731
sub get_seq_region_id {
  my $self = shift;
  my $slice = shift;
Graham McVicker's avatar
Graham McVicker committed
732

Ian Longden's avatar
Ian Longden committed
733
  if(!$slice || !ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
734 735
    throw('Slice argument is required');
  }
736
  
737
  my $seq_region_name = $slice->seq_region_name();
738
  my $key = $seq_region_name.":".$slice->coord_system->dbID();
739
  my $arr = $self->{'sr_name_cache'}->{"$key"};
740

741 742
  if( $arr ) {
    return $arr->[0];
743 744
  }

745
  my $cs_id = $slice->coord_system->dbID();
746 747 748 749 750 751

  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
752 753 754
  $sth->bind_param(1,"$seq_region_name",SQL_VARCHAR);
  $sth->bind_param(2,$cs_id,SQL_INTEGER);
  $sth->execute();
755 756 757

  if($sth->rows() != 1) {
    throw("Non existant or ambigous seq_region:\n" .
758 759 760
          "  coord_system=[$cs_id],\n" .
          "  name=[$seq_region_name],\n");

761 762 763 764 765 766
  }

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

  #cache information for future requests
767
  $arr = [ $seq_region_id, $seq_region_name, $cs_id, $length ];
768 769 770 771

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

772
  return $seq_region_id;
Arne Stabenau's avatar
Arne Stabenau committed
773
}
774 775


Arne Stabenau's avatar
Arne Stabenau committed
776

777 778 779 780 781 782 783 784 785
=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
786
  Arg [3]    : bool $include_non_reference (optional)
787 788 789
               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
790 791
  Arg [4]    : int $include_duplicates (optional)
               If set duplicate regions will be returned.
792
               
793
               NOTE: if you do not use this option and you have a PAR
794 795 796
               (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.
797

798 799 800 801
  Arg[5]     : bool $include_lrg (optional)  (default 0)
               If set lrg regions will be returned aswell.


802 803 804
  Example    : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
               @contigs = @{$slice_adaptor->fetch_all('contig')};

Graham McVicker's avatar
Graham McVicker committed
805 806 807 808 809
               # 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)};
810 811 812 813 814 815

  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.
816 817
               If the coordinate system with the provided name and version
               does not exist an empty list is returned.
818
               If the coordinate system name provided is 'toplevel', all
819 820
               non-redundant toplevel slices are returned (note that any
               coord_system_version argument is ignored in that case).
821 822 823 824

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

825
  Returntype : listref of Bio::EnsEMBL::Slices
826
  Exceptions : none
827
  Caller     : general
828
  Status     : Stable
Web Admin's avatar
Web Admin committed
829 830 831

=cut

832 833 834 835 836
sub fetch_all {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift || '';

837
  my ($include_non_reference, $include_duplicates, $include_lrg) = @_;
Web Admin's avatar
Web Admin committed
838

839 840 841
  #
  # verify existance of requested coord system and get its id
  #
842 843 844
  my $csa       = $self->db->get_CoordSystemAdaptor();
  my $orig_cs   = $csa->fetch_by_name($cs_name, $cs_version);

845
  return [] if ( !$orig_cs );
846

847
  my %bad_vals=();
848

849

850 851 852
  #
  # Get a hash of non reference seq regions
  #
853
  if ( !$include_non_reference ) {
854
    my $sth =
855 856 857 858 859 860 861 862 863
      $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 = ?' );

864 865
    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();
866

867
    my ($seq_region_id);
868
    $sth->bind_columns( \$seq_region_id );
869

870
    while ( $sth->fetch() ) {
871 872 873
      $bad_vals{$seq_region_id} = 1;
    }
  }
874

875 876 877
  #
  # if we do not want lrg's then add them to the bad list;
  #
878 879
  if ( !$include_lrg ) {
    my $sth =
880 881 882 883 884 885 886 887 888
      $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 = ?' );

889 890
    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();