ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::TranscriptMapper | new () |
protected Bio::EnsEMBL::Mapper | _load_mapper () |
public List | cdna2genomic () |
public List | genomic2cdna () |
public List | cds2genomic () |
public List | pep2genomic () |
public List | genomic2cds () |
public List | genomic2pep () |
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.
Definition at line 34 of file TranscriptMapper.pm.
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 :
Description: loads the mapper Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : Internal Status : Stable
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 :
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
public List Bio::EnsEMBL::TranscriptMapper::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 :
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
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 :
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
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 :
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
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 :
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
public Bio::EnsEMBL::TranscriptMapper Bio::EnsEMBL::TranscriptMapper::new | ( | ) |
Arg [1] : Bio::EnsEMBL::Transcript $transcript The transcript for which a TranscriptMapper should be created. Example :
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
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 :
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