NAME¶

Bio::DB::GFF::Aggregator::wormbase_gene -- Wormbase gene aggregator

SYNOPSIS¶

  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['wormbase_gene','clone'],
                                 );
 -------------------------------------------------------------------------------------
 Aggregator method: transcript
 Main method:       Sequence
 Sub methods:       CDS UTR TSS PolyA
 -------------------------------------------------------------------------------------

DESCRIPTION¶

This aggregator was written to be compatible with the C elegans GFF files. It aggregates raw "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 "Sequence".

 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "transcript"
 Args    : none
 Status  : Public

 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list "CDS", "UTR", "TSS", "PolyA"
 Args    : none
 Status  : Public

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