Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::TranscriptMapper Class Reference

List of all members.


Class Summary

Synopsis

  my $trmapper = Bio::EnsEMBL::TranscriptMapper-\>new($transcript);

  @coords = $trmapper-\>cdna2genomic( 123, 554 );

  @coords = $trmapper-\>genomic2cdna( 141, 500, -1 );

  @coords = $trmapper-\>genomic2cds( 141, 500, -1 );

  @coords = $trmapper-\>pep2genomic( 10, 60 );

  @coords = $trmapper-\>genomic2pep( 123, 400, 1 );

Description

This is a utility class which can be used to perform coordinate conversions
between a number of coordinate systems relating to transcripts.
 

Definition at line 29 of file TranscriptMapper.pm.

Available Methods

protected Bio::EnsEMBL::Mapper _load_mapper ()
public List cdna2genomic ()
public List cds2genomic ()
public List genomic2cdna ()
public List genomic2cds ()
public List genomic2pep ()
public
Bio::EnsEMBL::TranscriptMapper 
new ()
public List pep2genomic ()

Method Documentation

protected Bio::EnsEMBL::Mapper Bio::EnsEMBL::TranscriptMapper::_load_mapper ( )
  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript for which a mapper should be created.
  Example    : my $mapper = _load_mapper($transcript);
  Description: loads the mapper
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : Internal
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::cdna2genomic ( )
  Arg [1]    : $start
               The start position in cdna coordinates
  Arg [2]    : $end
               The end position in cdna coordinates
  Example    : @cdna_coords = $transcript_mapper->cdna2genomic($start, $end);
  Description: Converts cdna coordinates to genomic coordinates.  The
               return value is a list of coordinates and gaps.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throws if no start or end
  Caller     : general
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::cds2genomic ( )
  Arg [1]    : int $start
               start position in cds coords
  Arg [2]    : int $end
               end position in cds coords
  Example    : @genomic_coords = $transcript_mapper->cds2genomic(69, 306);
  Description: Converts cds coordinates into genomic coordinates.  The
               coordinates returned are relative to the same slice that the
               transcript used to construct this TranscriptMapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Gap and
               Bio::EnsEMBL::Mapper::Coordinate objects
  Exceptions : throws if no end
  Caller     : general
  Status     : at risk
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::genomic2cdna ( )
  Arg [1]    : $start
               The start position in genomic coordinates
  Arg [2]    : $end
               The end position in genomic coordinates
  Arg [3]    : $strand
               The strand of the genomic coordinates (default value 1)
  Example    : @coords = $trans_mapper->genomic2cdna($start, $end, $strnd);
  Description: Converts genomic coordinates to cdna coordinates.  The
               return value is a list of coordinates and gaps.  Gaps
               represent intronic or upstream/downstream regions which do
               not comprise this transcripts cdna.  Coordinate objects
               represent genomic regions which map to exons (utrs included).
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throws if start, end or strand not defined
  Caller     : general
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::genomic2cds ( )
  Arg [1]    : int $start
               The genomic start position
  Arg [2]    : int $end
               The genomic end position
  Arg [3]    : int $strand
               The genomic strand
  Example    : @cds_coords = $trans_mapper->genomic2cds($start, $end, $strand);
  Description: Converts genomic coordinates into CDS coordinates of the
               transcript that was used to create this transcript mapper.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throw if start, end or strand not defined
  Caller     : general
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::genomic2pep ( )
  Arg [1]    : $start
               The start position in genomic coordinates
  Arg [2]    : $end
               The end position in genomic coordinates
  Arg [3]    : $strand
               The strand of the genomic coordinates
  Example    : @pep_coords = $transcript->genomic2pep($start, $end, $strand);
  Description: Converts genomic coordinates to peptide coordinates.  The
               return value is a list of coordinates and gaps.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throw if start, end or strand not defined
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::TranscriptMapper Bio::EnsEMBL::TranscriptMapper::new ( )
  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript for which a TranscriptMapper should be created.
  Example    : $trans_mapper = Bio::EnsEMBL::TranscriptMapper->new($transcript)
  Description: Creates a TranscriptMapper object which can be used to perform
               various coordinate transformations relating to transcripts.
               Note that the TranscriptMapper uses the transcript state at the
               time of creation to perform the conversions, and that a new
               TranscriptMapper must be created if the Transcript is altered.
               'Genomic' coordinates are coordinates which are relative to the
               slice that the Transcript is on.
  Returntype : Bio::EnsEMBL::TranscriptMapper
  Exceptions : throws if a transcript is not an argument
  Caller     : Transcript::get_TranscriptMapper
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::TranscriptMapper::pep2genomic ( )
  Arg [1]    : int $start
               start position in peptide coords
  Arg [2]    : int $end
               end position in peptide coords
  Example    : @genomic_coords = $transcript_mapper->pep2genomic(23, 102);
  Description: Converts peptide coordinates into genomic coordinates.  The
               coordinates returned are relative to the same slice that the
               transcript used to construct this TranscriptMapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Gap and
               Bio::EnsEMBL::Mapper::Coordinate objects
  Exceptions : throws if no end
  Caller     : general
  Status     : Stable
 
Code:
click to view

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