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Bio::DB::GFF::Aggregator::transcript.3pm

NAME

Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator

SYNOPSIS

   use Bio::DB::GFF;
 
   # Open the sequence database
   my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                    -dsn     => 'dbi:mysql:elegans42',
                                    -aggregator => ['transcript','clone'],
                                  );
 
  -------------------------------------------------
  Aggregator method: transcript
  Main method:       transcript
  Sub methods:       exon CDS 5'UTR 3'UTR TSS PolyA
  -------------------------------------------------
 
 

DESCRIPTION

Bio::DB::GFF::Aggregator::transcript is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw "``exon'', ``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 ``Transcript'' (notice the capital ``T'').

Internally this module is very simple. To override it with one that recognizes a main feature named ``gene'', simply follow this template:

  my $db = Bio::DB::GFF->new(...etc...)
  my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
                                                 -main_method => 'gene',
                                                 -sub_parts => ['exon','CDS']);
  $db->add_aggregator($aggregator);
 
 

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 "intron", "exon" and "CDS"
  Args    : none
  Status  : Public
 
 

main_name

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