Bio::DB::GFF::Aggregator
wormbase_gene
Summary
Bio::DB::GFF::Aggregator::wormbase_gene -- Wormbase gene aggregator
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['wormbase_gene','clone'],
);
Description
Bio::DB::GFF::Aggregator::wormbase_gene is one of the default
aggregators, and was written to be compatible with the C elegans GFF
files. It aggregates raw ""exon", "CDS", "5'UTR", "3'UTR", "polyA"
and "TSS" features into "transcript" features. For compatibility with
the idiosyncrasies of the Sanger GFF format, it expects that the full
range of the transcript is contained in a main feature of type
"Sequence".
Methods
Methods description
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "transcript"
Args : none
Status : Public |
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list "exon", "CDS", "5'UTR", "3'UTR", "TSS", "PolyA"
Args : none
Status : Public |
Title : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "Sequence"
Args : none
Status : Public |
Methods code
sub method
{ 'transcript' } | sub require_whole_object
{ 1; } | sub part_names
{ return qw(exon CDS 5'UTR 3'UTR TSS PolyA); } | sub main_name
{ return 'Sequence'; } | General documentation
None reported.
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.