Bio::DB::GFF::Aggregator::wormbase_gene(3pm) | User Contributed Perl Documentation | Bio::DB::GFF::Aggregator::wormbase_gene(3pm) |
Bio::DB::GFF::Aggregator::wormbase_gene -- Wormbase gene aggregator
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'], ); ------------------------------------------------------------------------------------- Aggregator method: transcript Main method: Sequence Sub methods: CDS UTR TSS PolyA -------------------------------------------------------------------------------------
This aggregator was written to be compatible with the C elegans GFF files. It aggregates raw "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".
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 "CDS", "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
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.
2018-10-03 | perl v5.26.2 |