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Bio::DB::GFF::Aggregator::clone.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::GFF::Aggregator::clone -- Clone aggregatorSYNOPSIS
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 ----------------------------------------------------------------------------
DESCRIPTION
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''.aggregate
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.
method
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "clone" Args : none Status : Public
part_names
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
BUGS
None reported.SEE ALSO
Bio::DB::GFF, Bio::DB::GFF::AggregatorAUTHOR
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre