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Bio::DB::GFF::Aggregator::transcript.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::GFF::Aggregator::transcript -- Transcript 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: transcript Main method: transcript Sub methods: exon CDS 5'UTR 3'UTR TSS PolyA -------------------------------------------------
DESCRIPTION
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
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