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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 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.