Bio::DB::GFF::Aggregator::processed_transcript man page on Pidora

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Bio::DB::GFF::AggregatUserpCoBio::DB::GFF::Aggregator::processed_transcript(3)

NAME
       Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology
       Transcript

SYNOPSIS
	 use Bio::DB::GFF;

	 # Open the sequence database
	 my $db	     = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
					  -dsn	   => 'dbi:mysql:elegans42',
					  -aggregator => ['processed_transcript'],
					);

	------------------------------------------------------------------------
	Aggregator method: processed_transcript
	Main method:	   mRNA
	Sub methods:	   CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
	------------------------------------------------------------------------

DESCRIPTION
       Bio::DB::GFF::Aggregator::processed_transcript is one of the default
       aggregators, and was written to be compatible with the Sequence
       Ontology canonical gene.	 It aggregates raw "exon," "CDS",
       "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and
       "polyA_site" features into "mRNA" features.  The UTRs may also be named
       "untranslated_region," "five_prime_untranslated_region,"
       "three_prime_untranslated_region,", "5'-UTR," and other synonyms.

   method
	Title	: method
	Usage	: $aggregator->method
	Function: return the method for the composite object
	Returns : the string "processed_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 CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
	Args	: none
	Status	: Public

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

perl v5.14.1		     Bio::DB::GFF::Aggregator::processed_transcript(3)
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