SliceAdaptor.pm 17.9 KB
Newer Older
1 2

#
Simon Potter's avatar
pod  
Simon Potter committed
3
# Ensembl module for Bio::EnsEMBL::DBSQL::SliceAdaptor
4 5 6 7 8 9 10 11 12 13 14
#
# Cared for by Ewan Birney <ensembl-dev@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

15
Bio::EnsEMBL::DBSQL::SliceAdaptor - Adaptors for slices
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

=head1 SYNOPSIS
  



=head1 DESCRIPTION

Factory for getting out slices of assemblies. WebSlice is the highly
accelerated version for the web site.

=head1 AUTHOR - Ewan Birney

This modules is part of the Ensembl project http://www.ensembl.org

Email ensembl-dev@ebi.ac.uk

Describe contact details here

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut


# Let the code begin...


46
package Bio::EnsEMBL::DBSQL::SliceAdaptor;
47 48 49
use vars qw(@ISA);
use strict;

50 51

# Object preamble - inherits from Bio::EnsEMBL::Root
52 53
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Slice;
54
use Bio::EnsEMBL::DBSQL::DBAdaptor;
55

56

57
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
58 59


Graham McVicker's avatar
Graham McVicker committed
60
# new is inherited from BaseAdaptor
61

62

63

64
=head2 fetch_by_chr_start_end
65

66 67 68 69 70 71 72 73 74 75 76 77 78
  Arg [1]    : string $chr
               the name of the chromosome to obtain a slice for
  Arg [2]    : int $start
               the start basepair of the slice to obtain in chromosomal 
               coordinates
  Arg [3]    : int $end 
               the end basepair of the slice to obtain in chromosomal 
               coordinates
  Example    : $slice = $slice_adaptor->fetch_by_chr_start_end();
  Description: Creates a slice object on the given chromosome and coordinates.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
79 80 81

=cut

Graham McVicker's avatar
Graham McVicker committed
82
sub fetch_by_chr_start_end {
83 84
    my ($self,$chr,$start,$end) = @_;

85 86
    unless($chr) {
      $self->throw("chromosome name argument must be defined and not ''");
87 88
    }

89 90 91 92 93 94 95 96 97
    unless(defined $end) {   # Why defined?  Is '0' a valid end?
      $self->throw("end argument must be defined\n");
    }

    unless(defined $start) {
      $self->throw("start argument must be defined\n");
    }

    if($start > $end) {
98
      $self->throw("start must be less than end: parameters $chr:$start:$end");
99
    }
100
    
101
    my $slice;
102
    my $type = $self->db->assembly_type();
103

Graham McVicker's avatar
Graham McVicker committed
104
    $slice = Bio::EnsEMBL::Slice->new(
105 106 107 108
          -chr_name      => $chr,
          -chr_start     => $start,
          -chr_end       => $end,
          -assembly_type => $type,
109
          -adaptor       => $self
Graham McVicker's avatar
Graham McVicker committed
110
	 );
111 112 113 114 115 116

    return $slice;
}



117
=head2 fetch_by_contig_name
118

Graham McVicker's avatar
Graham McVicker committed
119 120 121 122 123 124 125 126 127 128 129
  Arg [1]    : string $name
               the name of the contig to obtain a slice for
  Arg [2]    : (optional) int $size
               the size of the flanking regions to obtain (aka context size)
  Example    : $slc = $slc_adaptor->fetch_by_contig_name('AB000878.1.1.33983');
  Description: Creates a slice object around the specified contig.  
               If a context size is given, the slice is extended by that 
               number of basepairs on either side of the contig.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
130 131 132

=cut

133
sub fetch_by_contig_name {
Graham McVicker's avatar
Graham McVicker committed
134
   my ($self,$name, $size) = @_;
135 136 137

   if( !defined $size ) {$size=0;}

Graham McVicker's avatar
Graham McVicker committed
138
   my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_contig($name);
139

140 141 142 143 144 145 146 147
   $start -= $size;
   $end += $size;

   if($start < 1) {
     $start  = 1;
   }

   return $self->fetch_by_chr_start_end($chr_name, $start, $end);
Graham McVicker's avatar
Graham McVicker committed
148 149 150 151
 }



Graham McVicker's avatar
Graham McVicker committed
152
=head2 fetch_by_fpc_name
Graham McVicker's avatar
Graham McVicker committed
153

Graham McVicker's avatar
Graham McVicker committed
154 155 156 157 158 159 160
  Arg [1]    : string $fpc_name
  Example    : my $slice = $slice_adaptor->fetch_by_fpc_name('NT_004321');
  Description: Creates a Slice on the region of the assembly where 
               the specified FPC (super) contig lies.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
Graham McVicker's avatar
Graham McVicker committed
161 162 163 164 165

=cut

sub fetch_by_fpc_name {
    my ($self,$fpc_name) = @_;
Arne Stabenau's avatar
Arne Stabenau committed
166 167 168
    
    my( $p, $f, $l ) = caller; 
    $self->warn( "$f:$l calls deprecated method fetch_by_fpc_name. Please use fetch_by_supercontig_name instead" );
Graham McVicker's avatar
Graham McVicker committed
169

Arne Stabenau's avatar
Arne Stabenau committed
170 171
    $self->fetch_by_supercontig_name( $fpc_name ); 
}
Graham McVicker's avatar
Graham McVicker committed
172

Arne Stabenau's avatar
Arne Stabenau committed
173 174 175 176 177 178
sub fetch_by_supercontig_name {
  my ($self,$supercontig_name) = @_;
  
  my $assembly_type = $self->db->assembly_type();
  
  my $sth = $self->db->prepare("
179 180
        SELECT chr.name, a.superctg_ori, MIN(a.chr_start), MAX(a.chr_end)
        FROM assembly a, chromosome chr
Arne Stabenau's avatar
Arne Stabenau committed
181 182
        WHERE superctg_name = ?
        AND type = ?
183
        AND chr.chromosome_id = a.chromosome_id
Graham McVicker's avatar
Graham McVicker committed
184 185 186
        GROUP by superctg_name
        ");

Arne Stabenau's avatar
Arne Stabenau committed
187 188 189 190 191 192 193 194 195 196 197 198
  $sth->execute( $supercontig_name, $assembly_type );
  
  my ($chr, $strand, $slice_start, $slice_end) = $sth->fetchrow_array;
  
  my $slice;
  
  $slice = new Bio::EnsEMBL::Slice
    (
     -chr_name => $chr,
     -chr_start =>$slice_start,
     -chr_end => $slice_end,
     -strand => $strand,
199 200
     -assembly_type => $assembly_type,
     -adaptor => $self
Arne Stabenau's avatar
Arne Stabenau committed
201 202 203 204 205
    );
  
  return $slice;
}

Graham McVicker's avatar
Graham McVicker committed
206

Arne Stabenau's avatar
Arne Stabenau committed
207
=head2 list_overlapping_supercontigs
Graham McVicker's avatar
Graham McVicker committed
208

Arne Stabenau's avatar
Arne Stabenau committed
209 210 211 212 213 214 215 216 217
  Arg [1]    : Bio::EnsEMBL::Slice $slice
               overlapping given Sice
  Example    : 
  Description: return the names of the supercontigs that overlap given Slice.  
  Returntype : listref string
  Exceptions : none
  Caller     : general

=cut
Graham McVicker's avatar
Graham McVicker committed
218 219


Arne Stabenau's avatar
Arne Stabenau committed
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237
sub list_overlapping_supercontigs {
   my ($self,$slice) = @_;
   my $sth = $self->db->prepare( "
      SELECT DISTINCT superctg_name
        FROM assembly a, chromosome c
       WHERE c.chromosome_id = a.chromosome_id 
         AND c.name = ?
         AND a.type = ?
         AND a.chr_end >= ?
         AND a.chr_start <= ?
       " );
   $sth->execute( $slice->chr_name(), $slice->assembly_type(),
		  $slice->chr_start(), $slice->chr_end() );

   my $result = [];
   while( my $aref = $sth->fetchrow_arrayref() ) {
     push( @$result, $aref->[0] );
   }
238

Arne Stabenau's avatar
Arne Stabenau committed
239 240
   return $result;
}
241 242


Web Admin's avatar
Web Admin committed
243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288
=head2 fetch_by_chr_band

 Title   : fetch_by_chr_band
 Usage   :
 Function: create a Slice representing a series of bands
 Example :
 Returns :
 Args    : the band name


=cut

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

    my $type = $self->db->assembly_type();

    my $sth = $self->db->prepare("
        select min(k.chr_start), max(k.chr_end)
          from chromosome as c, karyotype as k
         where c.chromosome_id = k.chromosome_id and c.name=? and k.band like ?
    ");
    $sth->execute( $chr, "$band%" );
    my ( $slice_start, $slice_end) = $sth->fetchrow_array;

    unless( defined($slice_start) ) {
       my $sth = $self->db->prepare("
           select min(k.chr_start), max(k.chr_end)
             from chromosome as c, karyotype as k
            where c.chromosome_id = k.chromosome_id and k.band like ?
       ");
       $sth->execute( "$band%" );
       ( $slice_start, $slice_end) = $sth->fetchrow_array;
    }

    return new Bio::EnsEMBL::Slice
      (
       -chr_name  => $chr,
       -chr_start => $slice_start,
       -chr_end   => $slice_end,
       -strand    => 1,
       -assembly_type => $type
      );
}


Graham McVicker's avatar
Graham McVicker committed
289 290
=head2 fetch_by_clone_accession

Graham McVicker's avatar
Graham McVicker committed
291 292 293 294 295 296 297 298 299 300 301
  Arg [1]    : string $clone 
               the embl accession of the clone object to retrieve
  Arg [2]    : (optional) int $size
               the size of the flanking regions to obtain around the clone 
  Example    : $slc = $slc_adaptor->fetch_by_clone_accession('AC000012',1000);
  Description: Creates a Slice around the specified clone.  If a context size 
               is given, the Slice is extended by that number of basepairs on 
               either side of the clone.  Throws if the clone is not golden.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if the clone is not in the assembly 
  Caller     : general
302 303 304

=cut

Graham McVicker's avatar
Graham McVicker committed
305
sub fetch_by_clone_accession{
306 307 308
   my ($self,$clone,$size) = @_;

   if( !defined $clone ) {
Graham McVicker's avatar
Graham McVicker committed
309
     $self->throw("Must have clone to fetch Slice of clone");
310 311 312
   }
   if( !defined $size ) {$size=0;}

313
   my $type = $self->db->assembly_type()
314 315 316 317 318
    or $self->throw("No assembly type defined");

   my $sth = $self->db->prepare("SELECT  c.name,
                        a.chr_start,
                        a.chr_end,
319
                        chr.name 
320 321
                    FROM    assembly a, 
                        contig c, 
322 323
                        clone  cl,
                        chromosome chr
324 325 326
                    WHERE c.clone_id = cl.clone_id
                    AND cl.name = '$clone'  
                    AND c.contig_id = a.contig_id 
327 328
                    AND a.type = '$type'
                    AND chr.chromosome_id = a.chromosome_id
329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345
                    ORDER BY a.chr_start"
                    );
   $sth->execute();
 
   my ($contig,$start,$end,$chr_name); 
   my $counter; 
   my $first_start;
   while ( my @row=$sth->fetchrow_array){
       $counter++;
       ($contig,$start,$end,$chr_name)=@row;
       if ($counter==1){$first_start=$start;}      
   }

   if( !defined $contig ) {
       $self->throw("Clone is not on the golden path. Cannot build Slice");
   }
     
346 347 348 349 350 351 352 353
   $first_start -= $size;
   $end += $size;

   if($first_start < 1) {
     $first_start = 1;
   }

   my $slice = $self->fetch_by_chr_start_end($chr_name, $first_start, $end);
354 355 356 357 358
   return $slice;
}



Graham McVicker's avatar
Graham McVicker committed
359
=head2 fetch_by_transcript_stable_id
360

Graham McVicker's avatar
Graham McVicker committed
361 362 363 364 365 366 367 368 369 370 371 372 373 374
  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 
               number of basepairs on either side of the 
               transcript.  Throws if the transcript is not golden.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
375 376 377

=cut

Graham McVicker's avatar
Graham McVicker committed
378
sub fetch_by_transcript_stable_id{
379 380 381 382 383 384
  my ($self,$transcriptid,$size) = @_;

  # Just get the dbID, then fetch slice by that
  my $ta = $self->db->get_TranscriptAdaptor;
  my $transcript_obj = $ta->fetch_by_stable_id($transcriptid);
  my $dbID = $transcript_obj->dbID;
Graham McVicker's avatar
Graham McVicker committed
385 386
  
  return $self->fetch_by_transcript_id($dbID, $size);
387 388
}

389

Graham McVicker's avatar
Graham McVicker committed
390 391


Graham McVicker's avatar
Graham McVicker committed
392 393
=head2 fetch_by_transcript_id

Graham McVicker's avatar
Graham McVicker committed
394 395 396 397 398 399 400 401 402 403 404 405 406 407
  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);
  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. 
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown on incorrect args
  Caller     : general
408 409 410

=cut

Graham McVicker's avatar
Graham McVicker committed
411
sub fetch_by_transcript_id {
412
  my ($self,$transcriptid,$size) = @_;
Graham McVicker's avatar
Graham McVicker committed
413 414

  unless( defined $transcriptid ) {
Graham McVicker's avatar
Graham McVicker committed
415 416
    $self->throw("Must have transcriptid id to fetch Slice of transcript");
  }
Graham McVicker's avatar
Graham McVicker committed
417 418 419

  $size = 0 unless(defined $size);
   
Graham McVicker's avatar
Graham McVicker committed
420 421 422 423 424
  my $ta = $self->db->get_TranscriptAdaptor;
  my $transcript_obj = $ta->fetch_by_dbID($transcriptid);
  
  my %exon_transforms;
  
425
  my $emptyslice;
Graham McVicker's avatar
Graham McVicker committed
426 427 428 429 430 431 432 433 434 435 436
  for my $exon ( @{$transcript_obj->get_all_Exons()} ) {
    $emptyslice = Bio::EnsEMBL::Slice->new( '-empty'   => 1,
					    '-adaptor' => $self,
					    '-ASSEMBLY_TYPE' =>
					    $self->db->assembly_type);     
    my $newExon = $exon->transform( $emptyslice );
    $exon_transforms{ $exon } = $newExon;
  }
  
  $transcript_obj->transform( \%exon_transforms );
  
437 438
  my $start = $transcript_obj->start() - $size;
  my $end = $transcript_obj->end() + $size;
Graham McVicker's avatar
Graham McVicker committed
439
  
440 441 442
  if($start < 1) {
    $start = 1;
  }
443
  
444 445 446
  my $slice = $self->fetch_by_chr_start_end($emptyslice->chr_name,
					    $start, $end);
  return $slice;
447 448
}

449 450


Graham McVicker's avatar
Graham McVicker committed
451
=head2 fetch_by_transcript_stable_id
452

Graham McVicker's avatar
Graham McVicker committed
453 454 455 456 457 458 459 460 461 462 463 464 465
  Arg [1]    : string $geneid
               The stable id of the gene 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 gene (0 by default)
  Example    : $slc = $sa->fetch_by_transcript_stable_id('ENSG00000012123',10);
  Description: Creates a slice around the region of the specified gene. 
               If a context size is given, the slice is extended by that 
               number of basepairs on either side of the gene. 
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
466 467 468

=cut

Graham McVicker's avatar
Graham McVicker committed
469
sub fetch_by_gene_stable_id{
470 471 472 473 474 475 476
   my ($self,$geneid,$size) = @_;

   if( !defined $geneid ) {
       $self->throw("Must have gene id to fetch Slice of gene");
   }
   if( !defined $size ) {$size=0;}

Graham McVicker's avatar
Graham McVicker committed
477
   my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_gene($geneid);
478 479

   if( !defined $start ) {
480
     my $type = $self->db->assembly_type()
Graham McVicker's avatar
Graham McVicker committed
481
       or $self->throw("No assembly type defined");
Graham McVicker's avatar
Graham McVicker committed
482 483
     $self->throw("Gene is not on the golden path '$type'. " .
		  "Cannot build Slice.");
484 485
   }
     
486 487 488 489 490 491 492 493
   $start -= $size;
   $end += $size;
   
   if($start < 1) {
     $start = 1;
   }

   return $self->fetch_by_chr_start_end($chr_name, $start, $end);
494 495 496
}


497

Graham McVicker's avatar
Graham McVicker committed
498
=head2 fetch_by_chr_name
Graham McVicker's avatar
Graham McVicker committed
499

Graham McVicker's avatar
Graham McVicker committed
500 501 502 503 504 505
  Arg [1]    : string $chr_name
  Example    : $slice = $slice_adaptor->fetch_by_chr_name('20'); 
  Description: Retrieves a slice on the region of an entire chromosome
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if $chr_name arg is not supplied
  Caller     : general
Graham McVicker's avatar
Graham McVicker committed
506 507 508 509 510 511 512 513 514 515 516 517 518 519

=cut

sub fetch_by_chr_name{
   my ($self,$chr_name) = @_;

   unless( $chr_name ) {
       $self->throw("Chromosome name argument required");
   }

   my $chr_start = 1;
   
   #set the end of the slice to the end of the chromosome
   my $ca = $self->db()->get_ChromosomeAdaptor();
520
   my $chromosome = $ca->fetch_by_chr_name($chr_name);
Graham McVicker's avatar
Graham McVicker committed
521 522
   my $chr_end = $chromosome->length();

523 524 525 526 527 528 529 530 531 532 533 534
   my $type = $self->db->assembly_type();

   my $slice = Bio::EnsEMBL::Slice->new
     (
      -chr_name      => $chr_name,
      -chr_start     => 1,
      -chr_end       => $chr_end,
      -assembly_type => $type,
      -adaptor       => $self
     );

   return $slice;
Graham McVicker's avatar
Graham McVicker committed
535 536
}

Graham McVicker's avatar
Graham McVicker committed
537 538


539 540 541 542 543 544 545 546 547 548 549 550
=head2 fetch_by_mapfrag

 Title   : fetch_by_mapfrag
 Usage   : $slice = $slice_adaptor->fetch_by_mapfrag('20');
 Function: Creates a slice of a "mapfrag"
 Returns : Slice object
 Args    : chromosome name


=cut

sub fetch_by_mapfrag{
551
   my ($self,$mymapfrag,$flag,$size) = @_;
552 553 554

   $flag ||= 'fixed-width'; # alt.. 'context'
   $size ||= $flag eq 'fixed-width' ? 200000 : 0;
555
   unless( $mymapfrag ) {
556 557 558 559 560 561 562
       $self->throw("Mapfrag name argument required");
   }

   my( $chr_start,$chr_end);
  
   #set the end of the slice to the end of the chromosome
   my $ca = $self->db()->get_MapFragAdaptor();
563
   my $mapfrag = $ca->fetch_by_synonym($mymapfrag);
564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589
   return undef unless defined $mapfrag;

   if( $flag eq 'fixed-width' ) {
       my $halfsize = int( $size/2 );
       $chr_start = $mapfrag->seq_start - $halfsize;
       $chr_end   = $mapfrag->seq_start + $size - $halfsize;
   } else {
       $chr_start     = $mapfrag->seq_start - $size;
       $chr_end       = $mapfrag->seq_end   + $size;
   }
   my $type = $self->db->assembly_type();

   my $slice = Bio::EnsEMBL::Slice->new
     (
      -chr_name      => $mapfrag->seq,
      -chr_start     => $chr_start,
      -chr_end       => $chr_end,
      -assembly_type => $type,
      -adaptor       => $self
     );

   return $slice;
}



Graham McVicker's avatar
Graham McVicker committed
590 591 592 593 594 595 596 597 598 599 600 601 602 603 604


=head2 _get_chr_start_end_of_contig

 Title   : _get_chr_start_end_of_contig
 Usage   :
 Function: returns the chromosome name, absolute start and absolute end of the 
           specified contig
 Returns : returns chr,start,end
 Args    : contig id

=cut

sub _get_chr_start_end_of_contig {
    my ($self,$contigid) = @_;
605

Graham McVicker's avatar
Graham McVicker committed
606 607 608 609 610 611 612 613 614 615
   if( !defined $contigid ) {
       $self->throw("Must have contig id to fetch Slice of contig");
   }
   
   my $type = $self->db->assembly_type()
    or $self->throw("No assembly type defined");

   my $sth = $self->db->prepare("SELECT  c.name,
                        a.chr_start,
                        a.chr_end,
616 617
                        chr.name 
                    FROM assembly a, contig c, chromosome chr 
Graham McVicker's avatar
Graham McVicker committed
618 619
                    WHERE c.name = '$contigid' 
                    AND c.contig_id = a.contig_id 
620 621
                    AND a.type = '$type'
                    AND chr.chromosome_id = a.chromosome_id"
Graham McVicker's avatar
Graham McVicker committed
622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646
                    );
   $sth->execute();
   my ($contig,$start,$end,$chr_name) = $sth->fetchrow_array;

   if( !defined $contig ) {
     $self->throw("Contig $contigid is not on the golden path of type $type");
   }

   return ($chr_name,$start,$end);
}

=head2 _get_chr_start_end_of_gene

 Title   : get_Gene_chr_bp
 Usage   : 
 Function: 
 Returns :  
 Args    :


=cut


sub _get_chr_start_end_of_gene {
  my ($self,$geneid) =  @_;
647
  
Graham McVicker's avatar
Graham McVicker committed
648 649 650 651 652 653 654 655
  my $type = $self->db->assembly_type()
    or $self->throw("No assembly type defined");
  
  my $sth = $self->db->prepare("SELECT  
   if(a.contig_ori=1,(e.contig_start-a.contig_start+a.chr_start),
                    (a.chr_start+a.contig_end-e.contig_end)),
   if(a.contig_ori=1,(e.contig_end-a.contig_start+a.chr_start),
                    (a.chr_start+a.contig_end-e.contig_start)),
656
     chr.name
Graham McVicker's avatar
Graham McVicker committed
657 658 659 660 661
  
                    FROM    exon e,
                        transcript tr,
                        exon_transcript et,
                        assembly a,
662
                        gene_stable_id gsi,
663
                        chromosome chr
Graham McVicker's avatar
Graham McVicker committed
664 665 666 667 668
                    WHERE e.exon_id=et.exon_id 
                    AND et.transcript_id =tr.transcript_id 
                    AND a.contig_id=e.contig_id 
                    AND a.type = '$type' 
                    AND tr.gene_id = gsi.gene_id
669
                    AND gsi.stable_id = '$geneid'
670
                    AND a.chromosome_id = chr.chromosome_id" 
Graham McVicker's avatar
Graham McVicker committed
671 672
                    );
   $sth->execute();
673

Graham McVicker's avatar
Graham McVicker committed
674 675 676 677 678 679 680 681 682
   my ($start,$end,$chr);
   my @start;
   while ( my @row=$sth->fetchrow_array){
      ($start,$end,$chr)=@row;
       push @start,$start;
       push @start,$end;
   }   
   
   my @start_sorted=sort { $a <=> $b } @start;
683

Graham McVicker's avatar
Graham McVicker committed
684 685
   $start=shift @start_sorted;
   $end=pop @start_sorted;
686

Graham McVicker's avatar
Graham McVicker committed
687
   return ($chr,$start,$end);      
688
}
Graham McVicker's avatar
Graham McVicker committed
689

690
1;
Graham McVicker's avatar
Graham McVicker committed
691 692 693 694 695 696