Bio::DB::GFF::Aggregator transcript
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Summary
Bio::DB::GFF::Aggregator::transcript -- Transcript aggregator
Package variables
No package variables defined.
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 => ['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);
Methods
methodDescriptionCode
part_namesDescriptionCode
main_nameDescriptionCode
Methods description
methodcode    nextTop
 Title   : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "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 "intron", "exon" and "CDS"
Args : none
Status : Public
main_namecodeprevnextTop
 Title   : main_name
Usage : $aggregator->main_name
Function: return the method for the main component
Returns : the string "transcript"
Args : none
Status : Public
Methods code
methoddescriptionprevnextTop
sub method {
 'transcript'
}
part_namesdescriptionprevnextTop
sub part_names {
  return qw(exon CDS 5'UTR 3'UTR TSS PolyA);
}
main_namedescriptionprevnextTop
sub main_name {
  return 'transcript';
}

1;
__END__
}
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.