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":
  $ git clone git://github.com/agordon/fasta_ushuffle.git
  $ 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


Copyright (C) 2010 A. gordon (gordon@cshl.edu).

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
=======

uShuffle is distributed under the following license:
/* Copyright (c) 2007
 *   Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne.
 * All rights reserved.
 *
 * 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.
 * 2. 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.
 * 3. The names of its contributors may not be used to endorse or promote
 *      products derived from this software without specific prior written
 *      permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */


The "fasta_ushuffle" wrapper code (fasta_ushuffle.c and fasta_ushuffle.h) are:
 Copyright (C) 2011,2012 by A. Gordon ( gordon at cshl dot edu )
 licensed under the same license as uShuffle.