SliceAdaptor.pm 12.6 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,
Graham McVicker's avatar
Graham McVicker committed
109 110
          -adaptor       => $self->db->get_SliceAdaptor()
	 );
111 112 113 114 115 116

    return $slice;
}



117
=head2 fetch_by_contig_name
118

119
 Title   : fetch_by_contig_name
Graham McVicker's avatar
Graham McVicker committed
120 121 122 123 124
 Usage   : $slice = $slice_adptr->fetch_by_contig_name('AC000012.00001',1000);
 Function: Creates a slice around the the specified contig.  If a context 
           size is given, the slice is extended by that number of basepairs 
           on either side of the contig.
 Returns : Bio::EnsEMBL::Slice object 
125 126 127 128 129
 Args    : contig id, [context size in bp]


=cut

130
sub fetch_by_contig_name {
131 132 133 134
   my ($self,$contigid,$size) = @_;

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

135
   my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_contig($contigid);
136

137 138 139 140 141 142 143 144
   $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
145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
 }


=head2 fetch_by_fpc_name

 Title   : fetch_by_fpc_name
 Usage   :
 Function: create a Slice representing a complete FPC contig
 Example :
 Returns : 
 Args    : the FPC contig id.


=cut

sub fetch_by_fpc_name {
    my ($self,$fpc_name) = @_;

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

    my $sth = $self->db->prepare("
166 167
        SELECT chr.name, a.superctg_ori, MIN(a.chr_start), MAX(a.chr_end)
        FROM assembly a, chromosome chr
Graham McVicker's avatar
Graham McVicker committed
168 169
        WHERE superctg_name = '$fpc_name'
        AND type = '$type'
170
        AND chr.chromosome_id = a.chromosome_id
Graham McVicker's avatar
Graham McVicker committed
171 172 173 174 175 176 177 178 179 180 181 182 183
        GROUP by superctg_name
        ");

    $sth->execute;

    my ($chr, $strand, $slice_start, $slice_end) = $sth->fetchrow_array;

    my $slice;

    $slice = new Bio::EnsEMBL::Slice($chr,$slice_start,$slice_end,
                                     $strand,$type);

    return $slice;
184 185 186 187
}



Graham McVicker's avatar
Graham McVicker committed
188 189 190 191
=head2 fetch_by_clone_accession

 Title   : fetch_by_clone_accession
 Usage   : $slice = $slice_adaptor->fetch_by_clone_accession('AC000012',1000);
Graham McVicker's avatar
Graham McVicker committed
192 193 194
 Function: 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.
195 196 197 198 199
 Returns : Slice object 
 Args    : clone id, [context size in bp]

=cut

Graham McVicker's avatar
Graham McVicker committed
200
sub fetch_by_clone_accession{
201 202 203
   my ($self,$clone,$size) = @_;

   if( !defined $clone ) {
Graham McVicker's avatar
Graham McVicker committed
204
     $self->throw("Must have clone to fetch Slice of clone");
205 206 207
   }
   if( !defined $size ) {$size=0;}

208
   my $type = $self->db->assembly_type()
209 210 211 212 213
    or $self->throw("No assembly type defined");

   my $sth = $self->db->prepare("SELECT  c.name,
                        a.chr_start,
                        a.chr_end,
214
                        chr.name 
215 216
                    FROM    assembly a, 
                        contig c, 
217 218
                        clone  cl,
                        chromosome chr
219 220 221
                    WHERE c.clone_id = cl.clone_id
                    AND cl.name = '$clone'  
                    AND c.contig_id = a.contig_id 
222 223
                    AND a.type = '$type'
                    AND chr.chromosome_id = a.chromosome_id
224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
                    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");
   }
     
241 242 243 244 245 246 247 248
   $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);
249 250 251 252 253
   return $slice;
}



Graham McVicker's avatar
Graham McVicker committed
254
=head2 fetch_by_transcript_stable_id
255

Graham McVicker's avatar
Graham McVicker committed
256 257
 Title   : fetch_by_transcript_stable_id
 Usage   : $slice = $slice_adaptor->fetch_by_transcript_stable_id(
258 259 260 261 262 263 264 265 266 267 268
                                       'ENST00000302930',1000);
 Function: Creates a slice of the specified object.  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.
 Returns : Slice object 
 Args    : transcript stable ID, [context size in bp]


=cut

Graham McVicker's avatar
Graham McVicker committed
269
sub fetch_by_transcript_stable_id{
270 271 272 273 274 275
  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
276 277
  
  return $self->fetch_by_transcript_id($dbID, $size);
278 279
}

280

Graham McVicker's avatar
Graham McVicker committed
281 282 283 284
=head2 fetch_by_transcript_id

 Title   : fetch_by_transcript_id
 Usage   : $slice = $slice_adaptor->fetch_by_transcript_id(24,1000);
285 286 287 288 289 290 291 292 293
 Function: Creates a slice of the specified object.  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.
 Returns : Slice object 
 Args    : transcript dbID, [context size in bp]

=cut

Graham McVicker's avatar
Graham McVicker committed
294
sub fetch_by_transcript_id {
295
  my ($self,$transcriptid,$size) = @_;
Graham McVicker's avatar
Graham McVicker committed
296 297 298 299 300 301 302 303 304 305
  if( !defined $transcriptid ) {
    $self->throw("Must have transcriptid id to fetch Slice of transcript");
  }
  if( !defined $size ) {$size=0;}
  
  my $ta = $self->db->get_TranscriptAdaptor;
  my $transcript_obj = $ta->fetch_by_dbID($transcriptid);
  
  my %exon_transforms;
  
306
  my $emptyslice;
Graham McVicker's avatar
Graham McVicker committed
307 308 309 310 311 312 313 314 315 316 317
  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 );
  
318 319
  my $start = $transcript_obj->start() - $size;
  my $end = $transcript_obj->end() + $size;
Graham McVicker's avatar
Graham McVicker committed
320
  
321 322 323
  if($start < 1) {
    $start = 1;
  }
324
  
325 326 327
  my $slice = $self->fetch_by_chr_start_end($emptyslice->chr_name,
					    $start, $end);
  return $slice;
328 329
}

330

Graham McVicker's avatar
Graham McVicker committed
331
=head2 fetch_by_gene_stable_id
332

Graham McVicker's avatar
Graham McVicker committed
333
 Title   : fetch_by_gene_stable_id
Graham McVicker's avatar
Graham McVicker committed
334 335 336 337
 Usage   : $slice = $slc_adptr->fetch_by_gene_stable_id('ENSG00000012123',100);
 Function: Creates a slice around the specified gene.  If a context size is 
           given, the slice is extended by that number of basepairs on either 
           side of the gene.  Throws if the gene is not golden.
338 339 340 341 342 343
 Returns : Slice object 
 Args    : gene id, [context size in bp]


=cut

Graham McVicker's avatar
Graham McVicker committed
344
sub fetch_by_gene_stable_id{
345 346 347 348 349 350 351
   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
352
   my ($chr_name,$start,$end) = $self->_get_chr_start_end_of_gene($geneid);
353 354

   if( !defined $start ) {
355
     my $type = $self->db->assembly_type()
Graham McVicker's avatar
Graham McVicker committed
356
       or $self->throw("No assembly type defined");
Graham McVicker's avatar
Graham McVicker committed
357 358
     $self->throw("Gene is not on the golden path '$type'. " .
		  "Cannot build Slice.");
359 360
   }
     
361 362 363 364 365 366 367 368
   $start -= $size;
   $end += $size;
   
   if($start < 1) {
     $start = 1;
   }

   return $self->fetch_by_chr_start_end($chr_name, $start, $end);
369 370 371
}


Graham McVicker's avatar
Graham McVicker committed
372
=head2 fetch_by_chr_name
373

Graham McVicker's avatar
Graham McVicker committed
374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393
 Title   : fetch_by_chr_name
 Usage   : $slice = $slice_adaptor->fetch_by_chr_name('20');
 Function: Creates a slice of an entire chromosome 
 Returns : Slice object 
 Args    : chromosome name


=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();
394
   my $chromosome = $ca->fetch_by_chr_name($chr_name);
Graham McVicker's avatar
Graham McVicker committed
395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414
   my $chr_end = $chromosome->length();

   return $self->fetch_by_chr_start_end($chr_name, $chr_start, $chr_end);
}



=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) = @_;
415

Graham McVicker's avatar
Graham McVicker committed
416 417 418 419 420 421 422 423 424 425
   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 = $self->db->prepare("SELECT  c.name,
                        a.chr_start,
                        a.chr_end,
426 427
                        chr.name 
                    FROM assembly a, contig c, chromosome chr 
Graham McVicker's avatar
Graham McVicker committed
428 429
                    WHERE c.name = '$contigid' 
                    AND c.contig_id = a.contig_id 
430 431
                    AND a.type = '$type'
                    AND chr.chromosome_id = a.chromosome_id"
Graham McVicker's avatar
Graham McVicker committed
432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456
                    );
   $sth->execute();
   my ($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) =  @_;
457
  
Graham McVicker's avatar
Graham McVicker committed
458 459 460 461 462 463 464 465
  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)),
466
     chr.name
Graham McVicker's avatar
Graham McVicker committed
467 468 469 470 471
  
                    FROM    exon e,
                        transcript tr,
                        exon_transcript et,
                        assembly a,
472
                        gene_stable_id gsi,
473
                        chromosome chr
Graham McVicker's avatar
Graham McVicker committed
474 475 476 477 478
                    WHERE e.exon_id=et.exon_id 
                    AND et.transcript_id =tr.transcript_id 
                    AND a.contig_id=e.contig_id 
                    AND a.type = '$type' 
                    AND tr.gene_id = gsi.gene_id
479
                    AND gsi.stable_id = '$geneid'
480
                    AND a.chromosome_id = chr.chromosome_id" 
Graham McVicker's avatar
Graham McVicker committed
481 482
                    );
   $sth->execute();
483

Graham McVicker's avatar
Graham McVicker committed
484 485 486 487 488 489 490 491 492
   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;
493

Graham McVicker's avatar
Graham McVicker committed
494 495
   $start=shift @start_sorted;
   $end=pop @start_sorted;
496

Graham McVicker's avatar
Graham McVicker committed
497
   return ($chr,$start,$end);      
498
}