NAME

Bio::ToolBox::Parser::ucsc::builder - Build gene and transcript SeqFeatures from UCSC formats

USAGE

Don't use this directly. This is an accessory module for the Bio::ToolBox::Parser::ucsc module.

It will take a line from a UCSC-formatted gene table (refFlat, genePred, knownGene) and assemble a hierarchical gene or transcript SeqFeature object.

METHODS

new

Pass an ARRAY reference representing the tab-delimited fields from a line read from UCSC-formatted file and the Bio::ToolBox::Parser::ucsc object itself. The method of parsing is determined by the number of elements.

build_transcript

build_gene

Methods for building the representative transcript and gene from the line data.

add_exons

add_utrs

add_cds

add_codons

Add relative subfeatures to a transcript.

find_existing_subfeature

Find the same subfeature when sharing is enabled.

update_attributes

add_unique_attribute

Add attributes.

name

name2

gene_name

chrom

txStart

txEnd

strand

cdsStart

cdsEnd

exonCount

exonStarts

exonEnds

type

refseq

note

status

completeness

ucsc

Read access to parsed values in the object.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.