Inheritance diagram for Bio::EnsEMBL::Compara::AlignSlice::Exon:

Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::AlignSlice::Exon;
  
  my $exon = new Bio::EnsEMBL::Compara::AlignSlice::Exon(
      );

SET VALUES

GET VALUES

Definition at line 21 of file Exon.pm.

Available Methods
protected	_deprecated_transform ()
protected String	_get_aligned_sequence_from_original_sequence_and_cigar_line ()
protected	_get_stable_entry_info ()
protected Bio::EnsEMBL::Mapper::Coordinate	_merge_ajoining_coords ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public	add_sub_SeqFeature ()
public void	add_supporting_features ()
public Bio::EnsEMBL::Exon	adjust_start_end ()
public Bio::EnsEMBL::Analysis	analysis ()
public	append_Exon ()
public Int	cdna_coding_end ()
public Int	cdna_coding_start ()
public Int	cdna_end ()
public Int	cdna_start ()
public String	cigar_line ()
public Int	coding_region_end ()
public Int	coding_region_start ()
public	contig ()
public String	coord_system_name ()
public Bio::EnsEMBL::Compara::AlignSlice::Exon	copy ()
public	created ()
public String	created_date ()
public Int	dbID ()
public String	display_id ()
public Int	end ()
public Int	end_phase ()
public Boolean	equals ()
public Bio::EnsEMBL::Exon	exon ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public void	find_supporting_evidence ()
public	flush_sub_SeqFeature ()
public	flush_supporting_features ()
public Int	frame ()
public	get_aligned_end ()
public	get_aligned_start ()
public Reference	get_all_alt_locations ()
public	get_all_DAS_Features ()
public Listreference	get_all_supporting_features ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public List	get_overlapping_Genes ()
public String	hashkey ()
public	id ()
public Int	is_constitutive ()
public Int	is_current ()
public Boolean	is_stored ()
public Int	length ()
public Nothing	load ()
public Bio::EnsEMBL::Compara::AlignSlice::Exon	map_Exon_on_Slice ()
public	modified ()
public String	modified_date ()
public void	move ()
public Bio::EnsEMBL::Compara::AlignSlice::Exon	new ()
public Bio::EnsEMBL::Feature	new_fast ()
public Int	original_rank ()
public Boolean	overlaps ()
public Bio::Seq	peptide ()
public Int	phase ()
public	prepend_Exon ()
public List	project ()
public List	project_to_slice ()
public Bio::Seq	seq ()
public Int	seq_region_end ()
public Unsigned	seq_region_length ()
public String	seq_region_name ()
public Int	seq_region_start ()
public Boolean	seq_region_strand ()
public String	seqname ()
public Bio::EnsEMBL::Slice	slice ()
public String	species ()
public String	stable_id ()
public Int	start ()
public Int	strand ()
public	sub_SeqFeature ()
public Hashref	summary_as_hash ()
public	temporary_id ()
public Bio::EnsEMBL::Gene	transfer ()
public Bio::EnsEMBL::Exon	transform ()
public	type ()
public String	version ()

Method Documentation

protected String Bio::EnsEMBL::Compara::AlignSlice::Exon::_get_aligned_sequence_from_original_sequence_and_cigar_line ( )

  Arg [1]    : string $original_sequence
  Arg [1]    : string $cigar_line
  Example    : $aligned_sequence = _get_aligned_sequence_from_original_sequence_and_cigar_line(
                   "CGTAACTGATGTTA", "3MD8M2D3M")
  Description: get gapped sequence from original one and cigar line
  Returntype : string $aligned_sequence
  Exceptions : thrown if cigar_line does not match sequence length
  Caller     : methodname

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon::append_Exon ( )

  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :

Code:

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public String Bio::EnsEMBL::Compara::AlignSlice::Exon::cigar_line ( )

  Arg[1]     : (optional) string $cigar_line
  Example    : $align_exon->cigar_line($cigar_line);
  Example    : $cigar_line = $align_exon->cigar_line();
  Description: Get/set the attribute cigar_line.
  Returntype : string
  Exceptions : none
  Caller     : object->methodname

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::copy ( )

  Arg[1]     : none
  Example    : my $new_align_slice = $old_align_slice->copy()
  Description: Creates a new Bio::EnsEMBL::AlignSlice::Exon object which
               is an exact copy of the calling object
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : 
  Caller     : $obeject->methodname

Code:

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public Bio::EnsEMBL::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::exon ( )

  Arg[1]     : (optional) Bio::EnsEMBL::Exon $original_exon
  Example    : $align_exon->exon($original_exon);
  Example    : $start = $align_exon->start();
  Description: Get/set the attribute start. This method is overloaded in order to
               return the starting postion on the AlignSlice instead of the
               original one. Original starting position may be retrieved using
               the SUPER::start() method or the orginal_start() method
  Returntype : Bio::EnsEMBL::Exon object
  Exceptions :

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon::get_aligned_end ( )

Undocumented method

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon::get_aligned_start ( )

Undocumented method

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::map_Exon_on_Slice ( )

  Arg[1]     : Bio::EnsEMBL::Mapper $from_mapper
  Arg[2]     : Bio::EnsEMBL::Mapper $to_mapper
  Example    : $align_exon->map_Exon_on_Slice($from_mapper, $to_mapper);
  Description: This function takes the original exon and maps it on the slice
               using the mappers.
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : returns undef if not enough information is provided
  Exceptions : returns undef if no piece of the original exon can be mapped.
  Caller     : new

Code:

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sub map_Exon_on_Slice {
  my ($self, $from_mapper, $to_mapper) = @_;
  my $original_exon = $self->exon;
  my $slice = $self->slice;

  if (!defined($slice) or !defined($original_exon) or !defined($from_mapper)) {
    return $self;
  }

  my @alignment_coords = $from_mapper->map_coordinates(
          "sequence", # $self->genomic_align->dbID,
          $original_exon->slice->start + $original_exon->start - 1,
          $original_exon->slice->start + $original_exon->end - 1,
          $original_exon->strand,
          "sequence" # $from_mapper->from
      );

  my $aligned_start;
  my $aligned_end;
  my $aligned_strand = 0;
  my $aligned_sequence = "";
  my $aligned_cigar = "";

  my $global_alignment_coord_start;
  my $global_alignment_coord_end;
  my $last_alignment_coord_end;
  my $last_alignment_coord_start;
  foreach my $alignment_coord (@alignment_coords) {
    ## $alignment_coord refer to genomic_align_block: (1 to genomic_align_block->length) [+]

    if ($alignment_coord->isa("Bio::EnsEMBL::Mapper::Coordinate")) {
      if ($alignment_coord->strand == 1) {
        if ($last_alignment_coord_end) {
          # Consider gap between this piece and the previous as a deletion
          my $length = $alignment_coord->start - $last_alignment_coord_end - 1;
          $aligned_cigar .= $length if ($length>1);
          $aligned_cigar .= "D" if ($length);
        }
        $last_alignment_coord_end = $alignment_coord->end;
        $global_alignment_coord_start = $alignment_coord->start if (!$global_alignment_coord_start);
        $global_alignment_coord_end = $alignment_coord->end;
      } else {
        if ($last_alignment_coord_start) {
          # Consider gap between this piece and the previous as a deletion
          my $length = $last_alignment_coord_start - $alignment_coord->end - 1;
          $aligned_cigar .= $length if ($length>1);
          $aligned_cigar .= "D" if ($length);
        }
        $last_alignment_coord_start = $alignment_coord->start;
        $global_alignment_coord_end = $alignment_coord->end if (!$global_alignment_coord_end);
        $global_alignment_coord_start = $alignment_coord->start;
      }
    } else {
      # This piece is outside of the alignment -> consider as an insertion
      my $length = $alignment_coord->length;
      $aligned_cigar .= $length if ($length>1);
      $aligned_cigar .= "I" if ($length);
      next;
    }

    if (!defined($to_mapper)) {
      ## Mapping on the alignment (expanded mode)
      if ($alignment_coord->strand == 1) {
        $aligned_strand = 1;
        $aligned_start = $alignment_coord->start if (!$aligned_start);
        $aligned_end = $alignment_coord->end;
      } else {
        $aligned_strand = -1;
        $aligned_start = $alignment_coord->start;
        $aligned_end = $alignment_coord->end if (!$aligned_end);
      }
      my $num = $alignment_coord->end - $alignment_coord->start + 1;
      $aligned_cigar .= $num if ($num > 1);
      $aligned_cigar .= "M" if ($num);

    } else {
      ## Mapping on the reference_Slice (collapsed mode)
      my @mapped_coords = $to_mapper->map_coordinates(
              "alignment", # $self->genomic_align->genomic_align_block->dbID,
              $alignment_coord->start,
              $alignment_coord->end,
              $alignment_coord->strand,
              "alignment" # $to_mapper->to
          );
      foreach my $mapped_coord (@mapped_coords) {
      ## $mapped_coord refer to reference_slice
        if ($mapped_coord->isa("Bio::EnsEMBL::Mapper::Coordinate")) {
          if ($alignment_coord->strand == 1) {
            $aligned_strand = 1;
            $aligned_start = $mapped_coord->start if (!$aligned_start);
            $aligned_end = $mapped_coord->end;
          } else {
            $aligned_strand = -1;
            $aligned_start = $mapped_coord->start;
            $aligned_end = $mapped_coord->end if (!$aligned_end);
          }
          my $num = $mapped_coord->end - $mapped_coord->start + 1;
          $aligned_cigar .= $num if ($num > 1);
          $aligned_cigar .= "M" if ($num);
        } else {
          my $num = $mapped_coord->end - $mapped_coord->start + 1;
          $aligned_cigar .= $num if ($num > 1);
          $aligned_cigar .= "I" if ($num);
        }
      }
    }
  }

  if ($aligned_strand == 0) {
    ## the whole sequence maps on a gap
    $self->{start} = undef;
    $self->{end} = undef;
    $self->{strand} = undef;
    return $self;
  }

  ## Set coordinates on "slice" coordinates
  $self->start($aligned_start - $slice->start + 1);
  $self->end($aligned_end - $slice->start + 1);
  $self->strand($aligned_strand);
  $self->cigar_line($aligned_cigar);

  if ($self->start > $slice->length or $self->end < 1) {
    $self->{start} = undef;
    $self->{end} = undef;
    $self->{strand} = undef;
    return $self;
  }

  return $self;
}

public Bio::EnsEMBL::Compara::AlignSlice::Exon Bio::EnsEMBL::Compara::AlignSlice::Exon::new ( )

  Arg[1]     : a reference to a hash where keys can be:
                 -exon
                 -adaptor
                 -reference_slice
  Example    : my $align_slice =
                   new Bio::EnsEMBL::Compara::AlignSlice(
                       -exon => $original_exon
                       -reference_slice => $reference_slice,
                   );
  Description: Creates a new Bio::EnsEMBL::AlignSlice::Exon object
  Returntype : Bio::EnsEMBL::Compara::AlignSlice::Exon object
  Exceptions : return an object with no start, end nor strand if the
               exon cannot be mapped on the reference Slice.

Code:

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Reimplemented from Bio::EnsEMBL::Exon.

public Int Bio::EnsEMBL::Compara::AlignSlice::Exon::original_rank ( )

  Arg[1]     : (optional) integer $original_rank
  Example    : $align_exon->original_rank(5);
  Example    : $original_rank = $align_exon->original_rank();
  Description: Get/set the attribute original_rank. The orignal_rank
               is the position of the orginal Exon in the original
               Transcript
  Returntype : integer
  Exceptions :

Code:

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public Bio::EnsEMBL::Compara::AlignSlice::Exon::prepend_Exon ( )

  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :

Code:

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public Bio::Seq Bio::EnsEMBL::Compara::AlignSlice::Exon::seq ( )

  Arg [1]    : none
  Example    : my $seq_str = $exon->seq->seq;
  Description: Retrieves the dna sequence of this Exon.
               Returned in a Bio::Seq object.  Note that the sequence may
               include UTRs (or even be entirely UTR).
  Returntype : Bio::Seq or undef
  Exceptions : warning if argument passed,
               warning if exon does not have attatched slice
               warning if exon strand is not defined (or 0)
  Caller     : general

Code:

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Reimplemented from Bio::EnsEMBL::Exon.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::AlignSlice::Exon::slice ( )

  Arg[1]     : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : $align_exon->slice($reference_slice);
  Example    : $reference_slice = $align_exon->slice();
  Description: Get/set the attribute slice. This method is overloaded in order
               to map original coordinates onto the reference Slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions :

Code:

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Reimplemented from Bio::EnsEMBL::Exon.

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

Bio/EnsEMBL/Compara/AlignSlice/Exon.pm

Class Summary

Synopsis

Available Methods

Method Documentation