CViT - Chromosome Viewing Tool
1/12/13 - Release 1.2
CViT is a Perl script used to quickly generate images that show features on
genomic sequence. It is intentionally simplistic and low-tech; there are
limitless possibilities for how one might view such data and CViT is
optimized for speed and ease of use over high-tech features.
Input is one or more files in GFF3 format.
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 or SVG 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
Most aspects of the image can be modified without touching the code.
See the ini file, config/cvit.ini.
Note that all names, types, and attributes in the GFF are case-sensitive.
GD library (http://www.libgd.org)
cvit.pl - the main scripts
cvit.log - tracks behavior and errors
config/ - contains one or more .ini files
documentation/ - how to use CViT
examples/ - examples of CViT use
fonts/ - contains truetype fonts
ColorManager.pm - manages colors
ConfigManager.pm - manages the drawing options from .ini file
CvitImage.pm - holds base image
CvitLib.pm - library of general purpose functions
errorlog.pm - writes to cvit.log
FontManager.pm - manages fonts
GFFManager.pm - manages the GFF records
GlyphCalc.pm - calculates positions for all the glyphs
GlyphDrawer.pm - draws glyphs onto base image
rgb.txt - list of possible colors
See config/cvit.ini and the examples for more information about how to use CViT.
CViT was designed and developed by Ethalinda and Steven Cannon. The icon was
designed by Melanie Shaw.
1.2 - Fixed bugs in coordinate systems with floating point values and placement of
glyphs when chromosomes don't share the same start coordinate.
1.1 - Code clean-up, more and better error reporting, variable chromosome placement,
many bug fixes. Added support for SVG images.
1.0 - First stable release. Minor bug fixes. 'Measure' records can be
displayed as either ranges or positions. Value for 'measure'
records can be distance from chromosome as well as heatmap colors
and histograms. Added web utility cvit-maker to distribution.
b2.0 - Made more consistent, added several drawing options, all options
in .ini file can be changed on the command line.
b1.3 - Improved ruler, including addition of fractional units (e.g.
Cytological McClintock units). Added ability to increase space to
left or right of the chromosome set. Writes only one label if
multiple labeled glyphs are printed at one location. Bug fixes.
b1.2 - Added grayscale colors for heatmaps, better error reporting, many
b1.1 - Truetype font support and better placement of text, features for
cytogentic maps, ruler can run backward
b1.0.1 - A few minor bug fixes. Added a legend image and file of feature
b1.0 - Initial SourceForge release