NAME¶
Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
SYNOPSIS¶
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['coding'],
);
------------------------------------------------------------------------
Aggregator method: coding
Main method: mRNA
Sub methods: CDS
------------------------------------------------------------------------
DESCRIPTION¶
Bio::DB::GFF::Aggregator::coding aggregates "CDS" features into a
feature called "coding" and was written to be compatible with the
Sequence Ontology canonical gene. The CDS features are expected to belong to a
parent of type "mRNA," but the aggregator will work even if this
isn't the case.
method¶
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "coding"
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 cds)
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) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself.