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Bio-EnsEMBL-112.0_55
River stage zero No dependents
/ Bio::EnsEMBL::TranscriptMapper

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

TranscriptMapper - A utility class used to perform coordinate conversions between a number of coordinate systems relating to transcripts

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.

Any transcript object given to TranscriptMapper should have a proper Slice object attached. The Slice provides vital information for the mapping process. After TranscriptMapper has been instantiated, changes to the supplied Transcript will not affect the Mapper's results.

METHODS

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

_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

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, where the coordinates
               are relative to the sequence region that the transcript used to construct
               this mapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throws if no start or end
  Caller     : general
  Status     : Stable

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).
               Note: A poorly formed Transcript will cause this method to
               malfunction.
  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

cds2genomic

  Arg [1]    : int $start
               start position in cds coords
  Arg [2]    : int $end
               end position in cds coords
  Arg [3]      boolean (0 or 1) $include_original_region
               option to include original input coordinate region mappings in the result
  Example    : @genomic_coords = $transcript_mapper->cds2genomic(69, 306);
  Description: Converts cds coordinates into genomic coordinates. Coordinates returned
               are relative to sequence region that the transcript used to construct
               this mapper 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

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 sequence region 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

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

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