Read Me

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CViT - Chromosome Viewing Tool
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10/20/10 - Release b1.0

CViT is a Perl script used to quickly generate images that show features on 
genomic sequence. It is intentionly simplistic and low-tech; there are limitless 
possibilities for how one might view such data.

Input is one or more files in GFF3 format.
(see http://www.sequenceontology.org/gff3.shtml)
One of these files must contain records describing one or more "chromosomes" 
(which could represent a psuedomolecule, BAC, contig, linkage group, any sort 
of contiguous stretch of DNA, or even a protein structure). These "chromosomes" 
are the backbone that the features are placed on.

Output is a PNG image.

CViT can be wrapped in other Perl scripts to extend its capability, or called by 
web pages to generate on-demand images. For example, BLAST hits can be displayed 
on a whole-genome view and displayed in a web browser.


Requirements:
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GD library (http://www.libgd.org)

Perl libraries:
  GD
  GD::Arrow
  GD::Image
  Config::IniFiles
  Data::Dumper


Files:
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cvit.pl     - the main scripts
cvit.log    - tracks behavior and errors, also used for debugging
errorlog.pm - writes to cvit.log
config/     - contains one or more .ini files
rgb.txt     - list of possible colors
examples/   - examples of CViT use

See config/cvit.ini and the examples for more information about how to use CViT.


Credits:
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CViT was designed and developed by Ethalinda and Steven Cannon. The icon was 
designed by Melanie Shaw.

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Changelog:
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b1.0 - initial SourceForge release