Bio::DB::GFF::AggregatUsergContributed Perl DBio::DB::GFF::Aggregator::gene(3)NAMEBio::DB::GFF::Aggregator::gene-- Sequence Ontology Geene
SYNOPSIS
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['gene'],
);
------------------------------------------------------------------------
Aggregator method: gene
Main method: mRNA
Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site
------------------------------------------------------------------------
DESCRIPTIONBio::DB::GFF::Aggregator::gene is identical to so_transcript, but is
used in those cases where you would like the name of the aggregated
feature to be "gene" rather than "processed_transcript". It aggregates
raw "exon," "CDS", "five_prime_UTR", "three_prime_UTR",
"transcription_start_site" and "polyA_site" features into "mRNA"
features. The UTRs may also be named "untranslated_region,"
"five_prime_untranslated_region," "three_prime_untranslated_region,",
"5'-UTR," and other synonyms.
method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "gene"
Args : none
Status : Public
part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
Args : none
Status : Public
main_name
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args : none
Status : Public
BUGS
None reported.
SEE ALSO
Bio::DB::GFF, Bio::DB::GFF::Aggregator
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2008 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
perl v5.14.1 2011-07-22 Bio::DB::GFF::Aggregator::gene(3)
