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.