/ 
Bio-BioStudio-2.11
River stage zero No dependents
/ BS_Cartoonist.pl

NAME

BS_Cartoonist.pl

VERSION

Version 2.10

DESCRIPTION

This utility takes a chromosome from the BioStudio genome repository and makes
 a vector image of its annotations.

ARGUMENTS

Required arguments:

 -C, --CHROMOSOME : The chromosome to be rendered.  Must be in the BioStudio
   genome repository.

Optional arguments:

 -F, --FACTOR : [def 10] The factor by which data will be scaled. Must be at
     least 2 - do you really want a 1:1 diagram of a chromosome?
 -L, --LEVELWIDTH : [def 50000] The bases represented per level of the diagram.
     A width of 50000 with a scaling factor of 10 will result in an image about
     5000 pixels wide.
 --REPEATLEFT : [def 1000] The number of bases from the previous level of the
     diagram that will be repeated in dashed lines, on the next level.
 --REPEATRIGHT : [def 1000] The number of bases at the end of each level of the
     diagram that will be repeated in dashed lines, on the next level.
 --START : [def 1] The first base to be displayed in the diagram. If it is not
     less than the length and equal to or greater than 1, it will default to 1.
 --STOP : [def chromosome length] The last base to be displayed in the
     diagram. If this number is larger than the length of the chromosome, it
     will default to chromosome length.
 -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.