Bio::DB::GFF::Aggregator::waba_alignment -- A WABA alignment
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 -------------------------------------------------------------------------------------
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
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "waba_alignment" Args : none Status : Public
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
None reported.
Bio::DB::GFF, Bio::DB::GFF::Aggregator
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
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