NAME

Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator

SYNOPSIS

  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::Aggregator

AUTHOR

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.