Inheritance diagram for Bio::EnsEMBL::LRGSlice:

Public Member Functions
public	new ()

public	stable_id ()

public	display_xref ()

public	feature_Slice ()

public	DESTROY ()

public	get_all_differences ()

Public Member Functions inherited from Bio::EnsEMBL::Slice
public Bio::EnsEMBL::Slice	new ()

public Bio::EnsEMBL::Slice	new_fast ()

public Bio::EnsEMBL::DBSQL::SliceAdaptor	adaptor ()

public String	seq_region_name ()

public Int	seq_region_start ()

public Int	seq_region_end ()

public Int	seq_region_length ()

public Bio::EnsEMBL::CoordSystem	coord_system ()

public String	source ()

public String	coord_system_name ()

public Int	centrepoint ()

public Int	start ()

public Int	end ()

public Int	strand ()

public String	name ()

public Int	length ()

public Int	is_reference ()

public Int	is_toplevel ()

public Int	has_karyotype ()

public Int	karyotype_rank ()

public Int	is_circular ()

public Bio::EnsEMBL::Slice	invert ()

public String	seq ()

public Txt	subseq ()

public Bio::EnsEMBL::Utils::Iterator	sub_Slice_Iterator ()

public String	assembly_exception_type ()

public Boolean	is_chromosome ()

public Hashref	get_base_count ()

public List	project ()

protected	_constrain_to_region ()

public Bio::EnsEMBL::Slice	expand ()

public Bio::EnsEMBL::Slice	constrain_to_seq_region ()

public Bio::EnsEMBL::Slice	sub_Slice ()

public Bio::EnsEMBL::Slice	seq_region_Slice ()

public Int	get_seq_region_id ()

public Scalar	get_genome_component ()

public Listref	get_all_Attributes ()

public Listref	get_all_PredictionTranscripts ()

public Listref	get_all_DnaAlignFeatures ()

public Listref	get_all_ProteinAlignFeatures ()

protected	_get_AlignFeatures ()

public Listref	get_all_SimilarityFeatures ()

public Listref	get_all_SimpleFeatures ()

public Listref	get_all_RepeatFeatures ()

public Bio::EnsEMBL::Variation::LDFeatureContainer	get_all_LD_values ()

protected	_get_VariationFeatureAdaptor ()

protected	_get_StructuralVariationFeatureAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_VariationAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_CoreAdaptor ()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor	_get_Adaptor ()

public Listref	get_all_VariationFeatures ()

public Listref	get_all_somatic_VariationFeatures ()

public Listref	get_all_somatic_VariationFeatures_by_source ()

public Listref	get_all_somatic_VariationFeatures_with_phenotype ()

public Listref	get_all_VariationFeatures_by_Population ()

public Listref	get_all_Genes ()

public Listref	get_all_Genes_by_type ()

public Listref	get_all_Genes_by_source ()

public Reference	get_all_Transcripts ()

public Listref	get_all_Transcripts_by_type ()

public Listref	get_all_Transcripts_by_source ()

public Reference	get_all_Exons ()

public Listref	get_all_KaryotypeBands ()

public Bio::EnsEMBL::RepeatMaskedSlice	get_repeatmasked_seq ()

protected void	_mask_features ()

public Listref	get_all_SearchFeatures ()

public Listref	get_all_AssemblyExceptionFeatures ()

public Listref	get_all_MiscFeatures ()

public Reference	get_all_MarkerFeatures ()

public Reference	get_MarkerFeatures_by_Name ()

public Reference	get_all_compara_DnaAlignFeatures ()

public Arrayref	get_all_compara_Syntenies ()

public Listref	get_all_Haplotypes ()

public	get_all_DASFactories ()

public	get_all_DASFeatures_dsn ()

public Hashref	get_all_DAS_Features ()

public	get_all_DASFeatures ()

public	old_get_all_DASFeatures ()

public Listref	get_all_ExternalFeatures ()

public Listref	get_all_DitagFeatures ()

public Hash	get_generic_features ()

public List	project_to_slice ()

public Reference	get_all_synonyms ()

public void	add_synonym ()

public String	feature_so_acc ()

public String	feature_so_term ()

public Hashref	summary_as_hash ()

public	slice ()

public	id ()

public	display_id ()

public	primary_id ()

public	desc ()

public	moltype ()

public	alphabet ()

public	accession_number ()

Detailed Description

Synopsis

$sa = $db->get_SliceAdaptor;
 
$slice =
  $sa->fetch_by_region( 'LRG', 'LRG3');
 
# get some attributes of the slice
my $seqname = $slice->seq_region_name();
my $start   = $slice->start();
my $end     = $slice->end();
 
# get the sequence from the slice
my $seq = $slice->seq();
 
# get some features from the slice
foreach $gene ( @{ $slice->get_all_Genes } ) {
  # do something with a gene
}
 
foreach my $feature ( @{ $slice->get_all_DnaAlignFeatures } ) {
  # do something with dna-dna alignments
}

Description

A LRG Slice object represents a region of a genome.  It can be used to retrieve
sequence or features from an area of interest.

Definition at line 37 of file LRGSlice.pm.

Member Function Documentation

◆ DESTROY()

public Bio::EnsEMBL::LRGSlice::DESTROY ( )

Undocumented method

Code:

click to view

◆ display_xref()

public Bio::EnsEMBL::LRGSlice::display_xref ( )

Undocumented method

Code:

click to view

◆ feature_Slice()

public Bio::EnsEMBL::LRGSlice::feature_Slice ( )

Undocumented method

Code:

click to view

◆ get_all_differences()

public Bio::EnsEMBL::LRGSlice::get_all_differences ( )

Undocumented method

Code:

click to view

sub get_all_differences{
  my $self = shift;
  
  my @results;
  
  # get seq_region_attrib diffs (always same-length substitutions)
  ################################################################
  
  my $sth = $self->adaptor->prepare(qq{
    SELECT sra.value
    FROM seq_region_attrib sra, attrib_type at
    WHERE at.code = '_rna_edit'
    AND at.attrib_type_id = sra.attrib_type_id
    AND sra.seq_region_id = ?
  });
  
  $sth->execute($self->get_seq_region_id);
  
  my $edit_string;
  
  $sth->bind_columns(\$edit_string);
  
  while($sth->fetch()) {
    my ($start, $end, $edit) = split " ", $edit_string;
    
    my $slice = $self->sub_Slice($start, $end);
    my $chr_proj = $slice->project("chromosome");
    my $ref_seq = '-';
    if(scalar @$chr_proj == 1) {
      $ref_seq = $chr_proj->[0]->[2]->seq;
    }
    
    
    my $diff = {
      'start' => $start,
      'end'   => $end,
      'type'  => 'substitution',
      'seq'   => $edit,
      'ref'   => $ref_seq,
    };
    
    push @results, $diff;
  }
  
  # get more complex differences via projections
  ##############################################
  
  # project the LRG slice to contig coordinates
  my @segs = @{$self->project("contig")};
  
  # if the LRG projects into more than one segment
  if(scalar @segs > 1) {
    
    my ($prev_end, $prev_chr_start, $prev_chr_end, $prev_was_chr);
    
    foreach my $seg(@segs) {
      
      # is this a novel LRG contig, or does it project to a chromosome?
      my @chr_proj = @{$seg->[2]->project("chromosome")};
      
      # if it is a normal contig
      if(scalar @chr_proj) {
        
        # check if there has been a deletion in LRG
        if($prev_was_chr && $prev_end == $seg->[0] - 1) {
          
          # check it's not just a break in contigs
          unless(
             ($chr_proj[0]->[2]->strand != $self->strand && $prev_chr_start == $chr_proj[0]->[2]->end + 1) ||
             ($chr_proj[0]->[2]->strand != $self->strand && $prev_chr_end == $chr_proj[0]->[2]->start - 1)
          ) {
            
            # now get deleted slice coords, depends on the strand rel to LRG
            my ($s, $e);
            
            # opposite strand
            if($chr_proj[0]->[2]->strand != $self->strand) {
              ($s, $e) = ($prev_chr_start - 1, $chr_proj[0]->[2]->end + 1);
            }
            
            # same strand
            else {
              ($s, $e) = ($prev_chr_end + 1, $chr_proj[0]->[2]->start - 1);
            }
            
            if($s > $e) {
              warn "Oops, trying to create a slice from $s to $e (could have been ", $prev_chr_start - 1, "-", $chr_proj[0]->[2]->end + 1, " or ", $prev_chr_end + 1, "-", $chr_proj[0]->[2]->start - 1, ")";
            }
            
            else {
              # get a slice representing the sequence that was deleted
              my $deleted_slice = $self->adaptor->fetch_by_region("chromosome", $chr_proj[0]->[2]->seq_region_name, $s, $e, $chr_proj[0]->[2]->strand);
              
              my $diff = {
                'start' => $seg->[0],
                'end'   => $prev_end,
                'type'  => 'deletion',
                'seq'   => '-',
                'ref'   => $deleted_slice->seq." ".$deleted_slice->start.'-'.$deleted_slice->end,
              };
              
              push @results, $diff;
            }
          }
        }
        
        $prev_was_chr = 1;
        
        $prev_chr_start = $chr_proj[0]->[2]->start;
        $prev_chr_end = $chr_proj[0]->[2]->end;
      }
      
      # if it is an LRG made-up contig for an insertion
      else {
        $prev_was_chr = 0;
        
        my $diff = {
          'start' => $seg->[0],
          'end'   => $seg->[1],
          'type'  => 'insertion',
          'seq'   => substr($self->seq, $seg->[0] - 1, $seg->[1] - $seg->[0] + 1),
          'ref'   => '-',
        };
        
        push @results, $diff;
      }
      
      $prev_end = $seg->[1];
    }
  }
  
  # return results sorted by start, then end position
  return [sort {$a->{start} <=> $b->{start} || $a->{end} <=> $b->{end}} @results];
}

◆ new()

public Bio::EnsEMBL::LRGSlice::new ( )

Undocumented method

Code:

click to view

◆ stable_id()

public Bio::EnsEMBL::LRGSlice::stable_id ( )

Undocumented method

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/LRGSlice.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ DESTROY()

◆ display_xref()

◆ feature_Slice()

◆ get_all_differences()

◆ new()

◆ stable_id()