NAME
Data::Random::Nucleotides - Generate random nucleotide strings.
VERSION
version 0.1
SYNOPSIS
use Data::Random::Nucleotides qw/:all/;
# Generate a string of 200 random A/C/G/T characters.
$nucs = rand_nuc ( size => 200 );
# Generate a string of random A/C/G/T between 20 and 500 characters.
$nucs = rand_nuc ( min => 20, max => 500 );
# Generate a string of 30 random A/C/G/T/N characters.
$nucs = rand_nuc ( size => 30, N=>1 );
# Generate a multi-lined string of 500 random A/C/G/T/N characters.
# The 500 characters will be split into lines of 70 characters each.
$nucs = rand_wrapped_nuc ( size => 500 );
# Generate a string containing a single FASTA-like sequence text.
$fasta = rand_fasta ( size => 200 ) ;DESCRIPTION
This module is a thin wrapper around Data::Random, providing utility functions to generate nucleotide sequence strings and FASTA-looking strings.
nucleotide strings contain only A/C/G/T (and possibly N) characters. FASTA strings are multi-lined nucleotide strings, with the first line containing a sequence id (see http://en.wikipedia.org/wiki/FASTA_format) .
METHODS
rand_nuc()
Returns a string of random nucleotides.
See rand_set in Data::Random for possible parameters (e.g. size, min, max).
If N is set, N will be a possible nucleoide. Otherwise - only A/C/G/T will be returned.
rand_wrapped_nuc()
Returns a multi-lined string of random nucleotides.
See rand_nuc for all possible parameters.
The returned string will be broken into lines of 70 characeters each.
rand_fasta()
Returns a random FASTA string.
First line begins with a > prefix, and a random sequence ID (alphanumeric).
The rest of the lines are random nucleotide strings, wrapped at 70 characters.
AUTHOR
Assaf Gordon, <gordon at cshl.edu>
TODO
- Finer control over nucleotide composition (currently: completely random)
- Generate FASTQ files
- Support lower-case nucleotides
- generate amino-acid codes
BUGS
Please report any bugs or feature requests to https://github.com/agordon/Data-Random-Nucleotides/issues
SEE ALSO
BioPerl provides similar functionality http://www.bioperl.org/wiki/Random_sequence_generation, but requires installing the BioPerl module.
LICENSE AND COPYRIGHT
Copyright 2012 Assaf Gordon.
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.