man Bio::DB::GFF::Aggregator::waba_alignment (3): 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.

AUTHOR

Lincoln Stein <[email protected]>.