Bio::DB::GFF::Aggregator processed_transcript
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Summary
Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript
Package variables
No package variables defined.
Included modules
Bio::DB::GFF::Aggregator
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 => ['processed_transcript'], ); ------------------------------------------------------------------------ Aggregator method: processed_transcript Main method: mRNA Sub methods: CDS 5'-UTR 3'-UTR transcription_start_site polyA_site ------------------------------------------------------------------------
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 "CDS", "5'-UTR", "3'-UTR",
"transcription_start_site" and "polyA_site" features into "gene"
features. The UTRs may also be named "untranslated_region,"
"five_prime_untranslated_region," or
"three_prime_untranslated_region."
Methods
main_nameDescriptionCode
methodDescriptionCode
part_namesDescriptionCode
Methods description
main_namecode    nextTop
 Title   : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "mRNA"
Args : none
Status : Public
methodcodeprevnextTop
 Title   : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "processed_transcript"
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
Methods code
main_namedescriptionprevnextTop
sub main_name {
  return 'mRNA';
}

1;
__END__
}
methoddescriptionprevnextTop
sub method {
 'processed_transcript'
}
part_namesdescriptionprevnextTop
sub part_names {
  return qw(CDS 5'-UTR 3'-UTR transcription_start_site 
	    polyA_site UTR five_prime_untranslated_region
	    three_prime_untranslated_region);
}
General documentation
BUGSTop
None reported.
SEE ALSOTop
Bio::DB::GFF, Bio::DB::GFF::Aggregator
AUTHORTop
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.