Bio::DB::GFF::Aggregator::transcript -- Transcript 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: transcript Main method: transcript Sub methods: exon CDS 5'UTR 3'UTR TSS PolyA ------------------------------------------------- Bio::DB::GFF::Aggregator::transcript 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 "Transcript" (notice the capital "T"). Internally this module is very simple. To override it with one that recognizes a main feature named "gene", simply follow this template: my $db = Bio::DB::GFF->new(...etc...) my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript', -main_method => 'gene', -sub_parts => ['exon','CDS']); $db->add_aggregator($aggregator);

method
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "transcript" Args : none Status : Public

part_names
Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the list "intron", "exon" and "CDS" Args : none Status : Public

main_name
Title : main_name Usage : $aggregator->main_name Function: return the method for the main component Returns : the string "transcript" 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.