Seeder::Background - Background object
Version 0.01
This module provides the get_background method.
use Seeder::Background;
my $background = Seeder::Background->new(
seed_width => "6",
hd_index_file => "6.index",
seq_file => "seq.fasta",
out_file => "seq.bkgd",
strand => "forward",
);
$background -> get_background;
None by default
Title : new
Usage : my $background = Seeder::Background->new(%args);
Function: constructor for the Seeder::Background object
Returns : new Seeder::Background object
Args :
seed_width # Seed width
hd_index_file # Index file
seq_file # Sequence file
out_file # Output file
strand # Strand (forward or revcom)
Title : get_background Usage : $background -> get_background; Function: coordinate the collection of Hamming distances Args : none
Title : _generate_word Usage : $self->_generate_word; Function: generate all combinations of nucleotides (A, C, G, T) Returns : reference to an array of words Args : none
Title : _get_distance Usage : $self->_get_distance; Function: collect distance occurences for each oligo Returns : reference to a 2D array of occurences Args : none
Title : _output_bkgd Usage : $self->_output_bkgd; Function: writes background Hamming distances to output file Args : none
François Fauteux, <ffauteux at cpan.org>
Please report any bugs or feature requests to bug-Seeder at rt.cpan.org, or at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Seeder. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
You can find documentation for this module with the perldoc command.
perldoc Seeder
You can also look for information at:
This algorithm was developed by François Fauteux, Mathieu Blanchette and Martina Strömvik. We thank the Perl Monks <http://www.perlmonks.org/> for their support.
Copyright 2008 François Fauteux, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
