Bio::DB::GFF::Aggregator::wormbase_gene(3pm)

Usage

  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
 -------------------------------------------------------------------------------------

Overview

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".

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 "CDS", "UTR", "TSS", "PolyA"
 Args    : none
 Status  : Public

main_name

 Title   : main_name
 Usage   : $aggregator->main_name
 Function: return the method for the main component
 Returns : the string "Sequence"
 Args    : none
 Status  : Public

Releases

8 releases since Debian 3.0 (Woody); the text changed 7 times.

3.0
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