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'], );
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 "Sequence: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 accomodate 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", "Sequence:Genomic_canonical") Args : none Status : Public
Lincoln Stein <email@example.com>.
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.