Bio::DB::GFF::AggregatUsercContributed Perl Bio::DB::GFF::Aggregator::clone(3)NAMEBio::DB::GFF::Aggregator::clone-- Clone 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: clone
Main method: -none-
Sub methods: Clone_left_end Clone_right_end region:Genomic_canonical
----------------------------------------------------------------------------
DESCRIPTIONBio::DB::GFF::Aggregator::clone is one of the default aggregators, and
was written to be compatible with the C elegans GFF files. It
aggregates raw "Clone_left_end", "Clone_right_end", and
"region:Genomic_canonical" features into composite features of type
"clone".
aggregate
Title : aggregate
Usage : $features = $a->aggregate($features,$factory)
Function: aggregate a feature list into composite features
Returns : an array reference containing modified features
Args : see L<Bio::DB::GFF::Aggregator>
Status : Public
The WormBase GFF model is unusual in that clones aren't identified as a
single feature with start and stop positions, but as two features, a
"left end" and a "right end". One or both of these features may be
absent. In order to accomodate this, the aggregator will return undef
for the start and/or stop if one or both of the ends are missing.
method
Title : method
Usage : $aggregator->method
Function: return the method for the composite object
Returns : the string "clone"
Args : none
Status : Public
part_names
Title : part_names
Usage : $aggregator->part_names
Function: return the methods for the sub-parts
Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
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.
perl v5.14.12011-07-22Bio::DB::GFF::Aggregator::clone(3)
