Bio::DB::GFF::Aggregator gene
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Summary
Bio::DB::GFF::Aggregator::gene -- Sequence Ontology Geene
Package variables
No package variables defined.
Inherit
Bio::DB::GFF::Aggregator
Synopsis
  use Bio::DB::GFF;
# Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['gene'], ); ------------------------------------------------------------------------ Aggregator method: gene Main method: mRNA Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site ------------------------------------------------------------------------
Description
Bio::DB::GFF::Aggregator::gene is identical to so_transcript, but is
used in those cases where you would like the name of the aggregated
feature to be "gene" rather than "processed_transcript". 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.
Methods
methodDescriptionCode
part_namesDescriptionCode
main_nameDescriptionCode
Methods description
methodcode    nextTop
 Title   : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "gene"
Args : none
Status : Public
part_namescodeprevnextTop
 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_namecodeprevnextTop
 Title   : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args : none
Status : Public
Methods code
methoddescriptionprevnextTop
sub method {
 'gene'
}
part_namesdescriptionprevnextTop
sub part_names {
  return qw(CDS transcription_start_site
	    polyA_site UTR five_prime_untranslated_region
	    three_prime_untranslated_region
	   five_prime_UTR three_prime_UTR exon);
}
main_namedescriptionprevnextTop
sub main_name {
  return 'mRNA';
}

1;
__END__
}
General documentation
BUGSTop
None reported.
SEE ALSOTop
Bio::DB::GFF, Bio::DB::GFF::Aggregator
AUTHORTop
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2008 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.