Bio::DB::GFF::Aggregator::transcript

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 AT cshl DOT 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.