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============================== CViT - Chromosome Viewing Tool ============================== Ethalinda Cannon ethy@a415software.com 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. (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 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 browser. 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. Requirements: ------------- Perl 5.8.8+ GD library (http://www.libgd.org) Perl libraries: GD GD::Arrow GD::Image GD::Text GD::SVG SVG Config::IniFiles Data::Dumper Files: ------ 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 pkgs/ 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. Credits: -------- CViT was designed and developed by Ethalinda and Steven Cannon. The icon was designed by Melanie Shaw. ******************************************************************************** Changelog: ---------- 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 bug fixes. 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 coordinates. b1.0 - Initial SourceForge release
Source: README, updated 2014-04-27

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