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NAME

Sanger::CGP::Vagrent::GenomicRegionDumper::AbstractGenomicRegionDumper - Abstract template class for dumping annotatable genomic regions

DESCRIPTION

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.

METHODS

Functions

dumpGeneRegions

Usage :
 $dumper->dumpGeneRegions($genomicRegion);
Function :

Finds annotatable gene footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.

Returns :

Boolean, true if successful

Params :

A Sanger::CGP::Vagrent::Data::GenomicRegion object

dumpExonRegions

Usage :
 $dumper->dumpExonRegions($genomicRegion);
Function :

Finds annotatable exon footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.

Returns :

Boolean, true if successful

Params :

A Sanger::CGP::Vagrent::Data::GenomicRegion object

dumpCodingExonRegions

Usage :
 $dumper->dumpCodingExonRegions($genomicRegion);
Function :

Finds annotatable protein coding exon footprints with in the specified GenomicRegion from the attached TranscriptSource and sends them to the GenomicRegionWriter.

Returns :

Boolean, true if successful

Params :

A Sanger::CGP::Vagrent::Data::GenomicRegion object

Abstract

_convertExonToAnnotatableExonicRegions

Usage :
 $dumper->_convertExonToAnnotatableExonicRegions($exon,$transcript,$process5Psplice,$process3Psplice);
Function :

Abstract method, needs to be overridden in subclass. Converts an exon into annotatable genomic regions

Returns :

An array of Sanger::CGP::Vagrent::Data::GenomicRegion objects

Params :

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

_convertExonToAnnotatableCodingExonicRegions

Usage :
 $dumper->_convertExonToAnnotatableCodingExonicRegions($exon,$transcript,$process5Psplice,$process3Psplice);
Function :

Abstract method, needs to be overridden in subclass. Converts an exon into annotatable genomic regions corresponding to coding sequence

Returns :

An array of Sanger::CGP::Vagrent::Data::GenomicRegion objects

Params :

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

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