egor 0.0.1

data/History.txt

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+== 0.0.1 2008-11-07
+
+* 1 major enhancement:
+  * Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+bin/egor
+config/website.yml
+config/website.yml.sample
+egor.gemspec
+lib/egor.rb
+lib/egor/cli.rb
+lib/enumerable_extensions.rb
+lib/environment.rb
+lib/environment_feature.rb
+lib/math_extensions.rb
+lib/narray_extensions.rb
+lib/nmatrix_extensions.rb
+script/console
+script/destroy
+script/generate
+script/txt2html
+test/test_egor.rb
+test/test_egor_cli.rb
+test/test_enumerable_extensions.rb
+test/test_environment_feature.rb
+test/test_helper.rb
+test/test_nmatrix_extensions.rb
+website/index.html
+website/index.txt
+website/javascripts/rounded_corners_lite.inc.js
+website/stylesheets/screen.css
+website/template.html.erb

data/PostInstall.txt

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+HELP/OPTIONS: egor -h
+
+For more information on egor, see http://egor.rubyforge.org
+
+

data/README.rdoc

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+= egor
+
+* http://egor.rubyforge.org
+
+== DESCRIPTION:
+
+egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
+
+== FEATURES/PROBLEMS:
+
+* No more segmentation fault
+* Full smoothing supported
+* Infinite number of environment features can be handled (in theory)
+
+== BASIC USAGE:
+
+    $ egor -l TEMLIST-file -c classdef.dat
+        or
+    $ egor -f TEM-file -c classdef.dat
+
+== OPTIONS:
+    --tem-file (-f) STRING: a tem file
+    --tem-list (-l) STRING: a list for tem files
+    --classdef (-c) STRING: a file for the defintion of environments (default: 'classdef.dat')
+    --outfile (-o) STRING: output filename ("allmat.dat" if not specified)
+    --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (not supported yet)
+    --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: (!!!not implemented yet!!!)
+        0 for using C and J only for structure
+        1 for both structure and sequence (default)
+    --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 (http://www.ruby-lang.org)
+* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
+* narray (http://narray.rubyforge.org/)
+* facets (http://facets.rubyforge.org/)
+* bio (http://bioruby.open-bio.org/)
+
+== INSTALL:
+
+    $ sudo gem install egor
+
+== 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.

data/Rakefile

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+%w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
+require File.dirname(__FILE__) + '/lib/egor'
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.new('egor', Egor::VERSION) do |p|
+  p.developer('Semin Lee', 'seminlee@gmail.com')
+  p.changes              = p.paragraphs_of("History.txt", 0..1).join("\n\n")
+  p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  p.rubyforge_name       = p.name # TODO this is default value
+  p.extra_deps         = [
+    ['narray','>= 0.5.9.5'],
+    ['bio',   '>= 1.2.1'],
+    ['facets','>= 2.4.5'],
+    ['simple_memoize', '>= 1.0.0'],
+  ]
+
+  p.extra_dev_deps = [
+    ['newgem', ">= #{::Newgem::VERSION}"]
+  ]
+
+  p.clean_globs |= %w[**/.DS_Store tmp *.log]
+  path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
+  p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
+  p.rsync_args = '-av --delete --ignore-errors'
+end
+
+require 'newgem/tasks' # load /tasks/*.rake
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# task :default => [:spec, :features]

data/bin/egor

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+#!/usr/bin/env ruby
+#
+#  Created on 2008-11-7.
+#  Copyright (c) 2008. All rights reserved.
+
+require File.expand_path(File.dirname(__FILE__) + "/../lib/egor")
+
+require "egor/cli"
+
+Egor::CLI.execute(ARGV)

data/config/website.yml

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+host: semin@rubyforge.org
+remote_dir: /var/www/gforge-projects/egor

data/config/website.yml.sample

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+host: unknown@rubyforge.org
+remote_dir: /var/www/gforge-projects/egor

data/egor.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{egor}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Semin Lee"]
+  s.date = %q{2008-11-10}
+  s.default_executable = %q{egor}
+  s.description = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
+  s.email = ["seminlee@gmail.com"]
+  s.executables = ["egor"]
+  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/enumerable_extensions.rb", "lib/environment.rb", "lib/environment_feature.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_egor.rb", "test/test_egor_cli.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_helper.rb", "test/test_nmatrix_extensions.rb", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.has_rdoc = true
+  s.homepage = %q{http://egor.rubyforge.org}
+  s.post_install_message = %q{PostInstall.txt}
+  s.rdoc_options = ["--main", "README.rdoc"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{egor}
+  s.rubygems_version = %q{1.3.1}
+  s.summary = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
+  s.test_files = ["test/test_helper.rb", "test/test_egor.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_nmatrix_extensions.rb", "test/test_egor_cli.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 2
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_runtime_dependency(%q<simple_memoize>, [">= 1.0.0"])
+      s.add_development_dependency(%q<newgem>, [">= 1.0.7"])
+      s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
+    else
+      s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
+      s.add_dependency(%q<newgem>, [">= 1.0.7"])
+      s.add_dependency(%q<hoe>, [">= 1.8.0"])
+    end
+  else
+    s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+    s.add_dependency(%q<bio>, [">= 1.2.1"])
+    s.add_dependency(%q<facets>, [">= 2.4.5"])
+    s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
+    s.add_dependency(%q<newgem>, [">= 1.0.7"])
+    s.add_dependency(%q<hoe>, [">= 1.8.0"])
+  end
+end