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

NAME

GD_Sequence_Subtraction.pl

VERSION

Version 5.56

DESCRIPTION

Given at least one nucleotide sequence and at least one short nucleotide
sequence, the Sequence_Subtraction script seeks to remove the short sequence
without changing the first frame translation of the large nucleotide sequence.
The short sequence can be a restriction enzyme recognition site, in which case
both the sequence and its reverse complement will be removed.

If an organism or RSCU file is provided, the script will take RSCU values into
account when making changes.

Output will be named according to the name of the input file, and will be
tagged with the _SS suffix.

USAGE

-e OR -s must be provided. If both are given both will be processed.

ARGUMENTS

Required arguments:

-in,  --input : a file containing nucleotide sequences.
-e,   --enzymes : a comma separated list of restriction enzymes that can be
  found in the enzyme file specified in the config directory. All restriction
  enzymes in the list will have their recognition sites removed from the input
  sequences.
OR
-rem,  --removes : a file containing short nucleotide sequences, or paths to
  several separated by commas. Any instances of the short sequences will be
  removed from the input sequences.

Optional arguments:

-org,   --organism : an organism whose RSCU table can be found in the config
  directory, or several separated by commas. flat is an option.
-rscu,  --rscu : path to an RSCU table generated by GD_Generate_RSCU_Table.pl,
  or several separated by commas.
-rev, --revcom : Whether or not to remove the sequence in both orientations.
  Assumed 1 for enzymes and 0 for other sequences.
-out, --output : path to an output directory
-f,   --format : output format of sequences
-s,   --split : output all sequences as separate files
-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.