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Bio-EnsEMBL-112.0_53
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/ 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

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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