= egor

* http://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 (default: 60)
    --noweight: calculate substitution counts with no weights
    --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 1.8.7 or above (http://www.ruby-lang.org)
* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)

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

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


== LICENSE:

(The MIT License)

Copyright (c) 2008 Semin Lee

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.