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Bio-BioStudio-2.11
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/ BS_ChromosomeAnalyzer.pl

NAME

  BS_ChromosomeAnalyzer.pl

VERSION

  Version 2.10

DESCRIPTION

  This utility provides a broad summary of features in a chromosome. If you ask
   for gbrowse output and have GBrowse enabled, every feature will have a link
   to itself in GBrowse.

  If you choose to analyze protein coding genes, this utility will tell you
   which genes are the smallest or the largest, which genes are essential,
   which genes overlap, which genes have introns, and where the biggest gene
   deserts are. It will also create a codon table and an RSCU value table and
   list any modifications to protein coding genes.

  If you choose to analyze non protein coding genes, transposons and repeat
   features, or chromosome features, you will get a list of features and their
   coordinates.

  If you choose to analyze restriction enzyme recognition sites, you will get a
   list of absent, unique, and rare (2-10 occurrences) restriction enzyme
   recognition sites.

ARGUMENTS

Required arguments:

  -CH,   --CHROMOSOME : The name of the chromosome to be analyzed

Optional arguments:

  -P,   --PCG   : Analyze protein coding genes
  -N,   --NPCG  : Analyze non protein coding genes
  -T,   --TR    : Analyze transposons and repeat features
  -BS,  --BS    : Analyze custom features specified in BioStudio
  -CF,  --CF    : Analyze other chromosome features
  -RE,  --RE    : Analyze restriction enzyme recognition sites
  -S,   --SCOPE : [seg, chrom (default) The scope of analysis. seg requires
                  START and STOP.
  -STA, --START : The first base for analysis;ignored unless SCOPE = seg
  -STO, --STOP  : The last base for analysis;ignored unless SCOPE = seg
  -O,   --OUTPUT   : Determines if output comes as gbrowse or txt (default)
  -h,   --help     : Display this message

COPYRIGHT AND LICENSE

Copyright (c) 2014, BioStudio developers 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 BioStudio 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.