egor

egor.rubyforge.org

DESCRIPTION:

egor: Esst GeneratOR, a program for calculating environment-specific substitution tables

FEATURES/PROBLEMS:

No more segmentation fault
Fast enough not to leave your place
Slow enough to check your emails or have some chats with your colleagues next you
Full smoothing supported
In theory, infinite number of environment features can be handled

INSTALL:

$ sudo gem install egor

BASIC USAGE:

$ egor -l TEMLIST-file -c classdef.dat
    or
$ egor -f TEM-file -c classdef.dat

OPTIONS:

--tem-file (-f) FILE: a tem file
--tem-list (-l) FILE: a list for tem files
--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
--outfile (-o) FILE: output filename (default 'allmat.dat')
--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting
--noweight: calculate substitution counts with no weights (default)
--smooth (-s) INTEGER:
    0 for parial smoothing (default)
    1 for full smoothing
--nosmooth: perform no smoothing operation
--cys (-y) INTEGER:
    0 for using C and J only for structure (default)
    1 for both structure and sequence
    2 for using only C for both
--output INTEGER:
    0 for raw counts (no-smoothing performed)
    1 for probabilities
    2 for log-odds (default)
--scale INTEGER: log-odds matrices in 1/n bit units (default 3)
--sigma DOUBLE: change the sigma value for smoothing (default 5)
--add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/=classes)
--penv: use environment-dependent frequencies for log-odds calculation (default false) (NOT implemented yet!!!)
--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
--verbose (-v) INTEGER
    0 for ERROR level (default)
    1 for WARN or above level
    2 for INFO or above level
    3 for DEBUG or above level
--version: print version
--help (-h): show help

REQUIREMENTS:

ruby 1.8.6 or above (www.ruby-lang.org)
rubygems 1.2.0 or above (rubyforge.org/projects/rubygems/)

Following RubyGems will be automatically installed if you have rubygems installed on your machine

narray (narray.rubyforge.org/)
facets (facets.rubyforge.org/)
bio (bioruby.open-bio.org/)
simple_memoize (github.com/JackDanger/simple_memoize/tree/master)

LICENSE:

(The MIT License)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ‘Software’), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED ‘AS IS’, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.