Sanger::CGP::Vagrent::GenomicRegionDumper::AbstractGenomicRegionDumper - Abstract template class for dumping annotatable genomic regions
This is an abstract template class for saving the regions of the genome that could be annotated to.
Using the supplied TranscriptSource, Transcripts that could generate annotations are selected and the relevent genomic regions are saved to the specified GenomicRegionWriter
Inherits from Sanger::CGP::Vagrent::Annotators::AbstractAnnotator.
$dumper->dumpGeneRegions($genomicRegion);
Finds annotatable gene footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.
Boolean, true if successful
$dumper->dumpExonRegions($genomicRegion);
Finds annotatable exon footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.
Boolean, true if successful
$dumper->dumpCodingExonRegions($genomicRegion);
Finds annotatable protein coding exon footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.
Boolean, true if successful
$dumper->_convertExonToAnnotatableExonicRegions($exon,$transcript,$process5Psplice,$process3Psplice);
Abstract method, needs to be overridden in subclass. Converts an exon into annotatable genomic regions
An array of Sanger::CGP::Vagrent::Data::GenomicRegion objects
A Sanger::CGP::Vagrent::Data::Exon object
A Sanger::CGP::Vagrent::Data::Transcript object
A boolean switch for applying splice site calculation rules to the 5' end of the exon
A boolean switch for applying splice site calculation rules to the 3' end of the exon
$dumper->_convertExonToAnnotatableCodingExonicRegions($exon,$transcript,$process5Psplice,$process3Psplice);
Abstract method, needs to be overridden in subclass. Converts an exon into annotatable genomic regions corresponding to coding sequence
An array of Sanger::CGP::Vagrent::Data::GenomicRegion objects
A Sanger::CGP::Vagrent::Data::Exon object
A Sanger::CGP::Vagrent::Data::Transcript object
A boolean switch for applying splice site calculation rules to the 5' end of the exon
A boolean switch for applying splice site calculation rules to the 3' end of the exon