Reference

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

NAME

Bio::DB::GFF::Aggregator::waba_alignment -- A WABA alignment

SYNOPSIS

  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['waba_alignment'],
                                 );
  # fetch the synthetic feature type "waba_alignment"
  my @waba    = $db->features('waba_alignment');
 -------------------------------------------------------------------------------------
 Aggregator method: waba_alignment
 Main method:       -none
 Sub methods:       nucleotide_match:waba_weak nucleotide_match:waba_strong 
                    nucleotide_match::waba_coding
 -------------------------------------------------------------------------------------

DESCRIPTION

Bio::DB::GFF::Aggregator::waba_alignment handles the type of alignments produced by Jim Kent's WABA program, and was written to be compatible with the C elegans GFF files. It aggregates the following feature types into an aggregate type of "waba_alignment":

   nucleotide_match:waba_weak
   nucleotide_match:waba_strong
   nucleotide_match:waba_coding

method

 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "waba_alignment"
 Args    : none
 Status  : Public

part_names

 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list "nucleotide_match:waba_weak", "nucleotide_match:waba_strong" and "nucleotide_match:waba_coding"
 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