Fasta-uShuffle is a wrapper for uShuffle.

uShuffle is: uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts Minghui Jiang*, James Anderson, Joel Gillespie and Martin Mayne BMC Bioinformatics 2008, 9:192 doi:10.1186/1471-2105-9-192 http://www.biomedcentral.com/1471-2105/9/192

uShuffle software is available at: http://digital.cs.usu.edu/~mjiang/ushuffle/

Installation

download the code, then run “make”: $g i t c l o n e g i t : / / g i t h u b . c o m / a g o r d o n / f a s t a_{u} s h u f f l e . g i t$ cd fasta_ushuffle $ make

If needed, copy the executables to your bin directory: $ sudo cp fasta_ushuffle ushuffle /usr/local/bin

Usage

$ ./fasta_ushuffle -h fasta_ushuffle: shuffles biological sequences while preserving the k-let counts.

VERSION 0.2

Uses the uShuffle library code by: Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne.

Usage: fasta_ushuffle [-r N] [-h] [-o] [-n N] [-k N] [-s N] < INPUT.FA > OUTPUT.FA

-h This help screen -o Print original (unshuffled) in output file. -k N specifies the let size -s N specifies the seed for random number generator. -n N For each input sequence, print N permutations (default is 1). Use this only for debugging. -r N Retry N times to find a new shuffle (Default is 10). After N retries, a warning is printed, and a non-shuffled sequence will be written.

Nucleotide sequences in the input FASTA file must be in a single line. This is a valid input file:

dummy1 AGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGAGTG dummy2 CTGAGAGTCACACATGATTTTACAACAACCATGAAG

This is not a valid input file:

dummy1 AGTAGTAGTAGTAGTAGTAGTAGTAG TAGTAGAGTG dummy2 CTGAGAGTCACACATGATTTTACAAC AACCATGAAG

Use fasta_formatter (from the FASTX-Toolkit) to re-format a multiline fasta file.

Example

$ ./fasta_ushuffle < test1.fa

hello ACGGGTTAAACCCGTTNN world AGAAGTGAGTGTTGAGTAAGTACATTAGA

LICENSE

Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,

 this list of conditions and the following disclaimer.

1. Redistributions in binary form must reproduce the above copyright notice,

 this list of conditions and the following disclaimer in the

 documentation and/or other materials provided with the distribution.

1. The names of its contributors may not be used to endorse or promote

 products derived from this software without specific prior written

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