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lib/BioX/SeqUtils/RandomSequence.pm  view on Meta::CPAN

=back

=head1 SCRIPTS

The package includes scripts for random dna, rna, dinucleotide, and protein 
sequences. The length and frequency parameters should always be integers.

To create a dinucleotide sequence:

    ./random-dna.pp                                      # Defaults: length 2, all frequencies 1
    ./random-dna.pp -a250 -c250 -g250 -t250              # Create broader distribution

To create a dna sequence:

    ./random-dna.pp -l21                                 # Defaults: all frequencies 1 ( p = .25 )
    ./random-dna.pp -l2200 -a23 -c27 -g27 -t23           # Enrich GC content with length 2200

To create a rna sequence:

    ./random-rna.pp -l100                                     
    ./random-rna.pp -l2200 -a23 -c27 -g27 -t23           

To create a protein sequence:

    ./random-protein.pp                                  # Defaults: length 2, all frequencies .25
    ./random-protein.pp -l2200 -a23 -c27 -g27 -t23       # Enrich underlying GC content, aa length 2200

To create a protein set (with common DNA shifted by one base):

    ./random-protein-set.pp                              # Defaults: length 2, all frequencies .25
    ./random-protein-set.pp -l2200 -a23 -c27 -g27 -t23   # Enrich underlying GC content 

Additionally, a "master script" uses a tYpe parameter for any:

    ./random-sequence.pp                                 # Type 2 dinucleotide
    ./random-sequence.pp -yd -l100                       # Type d dna
    ./random-sequence.pp -yr -l100                       # Type r rna
    ./random-sequence.pp -yp -l100                       # Type p protein
    ./random-sequence.pp -ys -l100                       # Type s protein set

This module uses Bio::Tools::CodonTable for translations, and the parameter s can be used to 
change from the default (1) "Standard":

    ./random-protein.pp -l2200 -s2                       # Non-standard codon table


=head1 CONFIGURATION AND ENVIRONMENT

None.

=head1 DEPENDENCIES

    Class::Std;
    Class::Std::Utils;
    Bio::Tools::CodonTable;

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

No bugs have been reported.

Please report any bugs or feature requests to
C<bug-biox-sequtils-randomsequence@rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org>.

=head1 AUTHOR

Roger A Hall  C<< <rogerhall@cpan.org> >>

=head1 LICENSE AND COPYRIGHT

Copyleft (c) 2009, Roger A Hall C<< <rogerhall@cpan.org> >>. All rights reserved.

This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself. See L<perlartistic>.


=head1 DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH
YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL
NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENCE, BE
LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL,
OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE
THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.

=cut

Option a	+int		frequency of nucleotide A
Option c	+int		frequency of nucleotide C
Option g	+int		frequency of nucleotide G
Option l	+int		length 
Option t	+int		frequency of nucleotide T
Option s	+int		codon table 
Option y	2,d,r,p,s	type (dinucleotide, dna, rna, protein, set)