| Bio::DB::GFF::Aggregator::clone(3pm) | User Contributed Perl Documentation | Bio::DB::GFF::Aggregator::clone(3pm) |
Bio::DB::GFF::Aggregator::clone -- Clone aggregator
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
-dsn => 'dbi:mysql:elegans42',
-aggregator => ['transcript','clone'],
);
----------------------------------------------------------------------------
Aggregator method: clone
Main method: -none-
Sub methods: Clone_left_end Clone_right_end region:Genomic_canonical
----------------------------------------------------------------------------
Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw "Clone_left_end", "Clone_right_end", and "region:Genomic_canonical" features into composite features of type "clone".
Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see L<Bio::DB::GFF::Aggregator> Status : Public
The WormBase GFF model is unusual in that clones aren't identified as a single feature with start and stop positions, but as two features, a "left end" and a "right end". One or both of these features may be absent. In order to accommodate this, the aggregator will return undef for the start and/or stop if one or both of the ends are missing.
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "clone" Args : none Status : Public
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
Args : none
Status : Public
None reported.
Bio::DB::GFF, Bio::DB::GFF::Aggregator
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.
| 2020-01-13 | perl v5.30.0 |