NAME
Bio::DB::GFF::Aggregator::coding -- The Coding Region Aggregator
SYNOPSIS
# 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
"processed_transcript"
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.