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:

* RT: CPAN's request tracker

http://rt.cpan.org/NoAuth/Bugs.html?Dist=Seeder

* AnnoCPAN: Annotated CPAN documentation

http://annocpan.org/dist/Seeder

* CPAN Ratings

http://cpanratings.perl.org/d/Seeder

* Search CPAN

http://search.cpan.org/dist/Seeder

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.