Reference

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

NAME

Bio::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
 ----------------------------------------------------------------------------

DESCRIPTION

Bio::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 accommodate 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 <[email protected]>.

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.

History