/ 
Bio-GeneDesign-5.56
River stage zero No dependents
/ GD_Generate_RSCU_Table.pl

NAME

GD_Generate_RSCU_Table.pl

VERSION

Version 5.56

DESCRIPTION

Given at least one protein-coding gene as input, the Generate_RSCU_Table
script generates a table of RSCU values that represents the bias in codon
usage.

Output will be named according to the name of the input file, and will be
named  "inputfilename_GDRSCU.rscu".

ARGUMENTS

Required arguments:

-i,   --input : a file containing nucleotide sequences.

Optional arguments:

-out, --output : path to an output directory
-org, --organism : an organism whose codon table can be found in the
    config directory, necessary if the organism being parsed doesn't use the
    standard codon table
    OR
-c,   --codontable : path to a codon table; necessary if the organism being
    parsed doesn't use the standard codon table
-h,   --help : Display this message.

COPYRIGHT AND LICENSE

Copyright (c) 2015, Sarah Richardson All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

* 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.

* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the GeneDesign developers 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 DEVELOPERS 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.