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Seeder-0.01
River stage zero No dependents
/ Seeder::Background

NAME

Seeder::Background - Background object

VERSION

Version 0.01

DESCRIPTION

This module provides the get_background method.

SYNOPSIS

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;

EXPORT

None by default

FUNCTIONS

new

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)

get_background

Title   : get_background
Usage   : $background -> get_background;
Function: coordinate the collection of Hamming distances
Args    : none

_generate_word

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

_get_distance

Title   : _get_distance
Usage   : $self->_get_distance;
Function: collect distance occurences for each oligo
Returns : reference to a 2D array of occurences
Args    : none

_output_bkgd

Title   : _output_bkgd
Usage   : $self->_output_bkgd;
Function: writes background Hamming distances to output file
Args    : none

AUTHOR

François Fauteux, <ffauteux at cpan.org>

BUGS

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.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc Seeder

You can also look for information at:

ACKNOWLEDGEMENTS

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 & LICENSE

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.

1 POD Error

The following errors were encountered while parsing the POD:

Around line 280:

Non-ASCII character seen before =encoding in 'François'. Assuming UTF-8