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lib/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm  view on Meta::CPAN

sub fetch_by_transcript_id {
  my ($self,$transcriptid,$size) = @_;

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

  my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
  my $transcript = $transcript_adaptor->fetch_by_dbID($transcriptid);

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

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



=head2 fetch_by_gene_stable_id

  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_gene_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.
               
               The slice will be created in the gene's native coordinate system
               and in the forward orientation.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : throw on incorrect args
               throw if transcript does not exist
  Caller     : general
  Status     : Stable

=cut

sub fetch_by_gene_stable_id {
  my ($self,$geneid,$size) = @_;

  throw('Gene argument is required.') if(!$geneid);

  my $gene_adaptor = $self->db->get_GeneAdaptor();
  my $gene = $gene_adaptor->fetch_by_stable_id($geneid);

  throw("Gene [$geneid] does not exist in DB.") if(!$gene);

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



=head2 fetch_by_Feature

  Arg [1]    : Bio::EnsEMBL::Feature $feat
               The feature to fetch the slice around
  Arg [2]    : int size (optional)
               The desired number of flanking basepairs around the feature.
               The size may also be provided as a percentage of the feature 
               size such as 200% or 80.5%.
  Example    : $slice = $slice_adaptor->fetch_by_Feature($feat, 100);
  Description: Retrieves a slice around a specific feature.  All this really
               does is return a resized version of the slice that the feature
               is already on. Note that slices returned from this method
               are always on the forward strand of the seq_region regardless of
               the strandedness of the feature passed in.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : throw if the feature does not have an attached slice
               throw if feature argument is not provided
  Caller     : fetch_by_gene_stable_id, fetch_by_transcript_stable_id,
               fetch_by_gene_id, fetch_by_transcript_id
  Status     : Stable

=cut

sub fetch_by_Feature{
  my ($self, $feature, $size) = @_;

  $size ||= 0;

  if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
    throw('Feature argument expected.');
  }

  my $slice = $feature->slice();
  if(!$slice || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice') )) {
    throw('Feature must be attached to a valid slice.');
  }


  my $fstart = $feature->start();
  my $fend   = $feature->end();
  if(!defined($fstart) || !defined($fend)) {
    throw('Feature must have defined start and end.');
  }

  #convert the feature slice coordinates to seq_region coordinates
  my $slice_start  = $slice->start();
  my $slice_end    = $slice->end();
  my $slice_strand = $slice->strand();
  if($slice_start != 1 || $slice_strand != 1) {
    if($slice_strand == 1) {
      $fstart = $fstart + $slice_start - 1;
      $fend   = $fend   + $slice_start - 1;
    } else {
      my $tmp_start = $fstart;
      $fstart = $slice_end - $fend      + 1;
      $fend   = $slice_end - $tmp_start + 1;
    }
  }

  ## Size may be stored as a %age of the length of the feature
  ## Size = 100% gives no context
  ## Size = 200% gives context - 50% the size of the feature either side of 
  ## feature

  $size = int( ($1-100)/200 * ($fend-$fstart+1) ) if( $size =~/([\d+\.]+)%/ );

  #return a new slice covering the region of the feature