egor 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/History.txt +4 -0
- data/Manifest.txt +32 -0
- data/PostInstall.txt +5 -0
- data/README.rdoc +88 -0
- data/Rakefile +32 -0
- data/bin/egor +10 -0
- data/config/website.yml +2 -0
- data/config/website.yml.sample +2 -0
- data/egor.gemspec +53 -0
- data/lib/egor/cli.rb +1063 -0
- data/lib/egor.rb +6 -0
- data/lib/enumerable_extensions.rb +11 -0
- data/lib/environment.rb +58 -0
- data/lib/environment_feature.rb +14 -0
- data/lib/math_extensions.rb +7 -0
- data/lib/narray_extensions.rb +21 -0
- data/lib/nmatrix_extensions.rb +24 -0
- data/script/console +10 -0
- data/script/destroy +14 -0
- data/script/generate +14 -0
- data/script/txt2html +71 -0
- data/test/test_egor.rb +11 -0
- data/test/test_egor_cli.rb +8 -0
- data/test/test_enumerable_extensions.rb +16 -0
- data/test/test_environment_feature.rb +11 -0
- data/test/test_helper.rb +2 -0
- data/test/test_nmatrix_extensions.rb +16 -0
- data/website/index.html +78 -0
- data/website/index.txt +48 -0
- data/website/javascripts/rounded_corners_lite.inc.js +285 -0
- data/website/stylesheets/screen.css +159 -0
- data/website/template.html.erb +50 -0
- metadata +154 -0
data/History.txt
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data/Manifest.txt
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History.txt
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Manifest.txt
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PostInstall.txt
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README.rdoc
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Rakefile
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bin/egor
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config/website.yml
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config/website.yml.sample
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egor.gemspec
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lib/egor.rb
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lib/egor/cli.rb
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lib/enumerable_extensions.rb
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lib/environment.rb
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lib/environment_feature.rb
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lib/math_extensions.rb
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lib/narray_extensions.rb
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lib/nmatrix_extensions.rb
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script/console
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script/destroy
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script/generate
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script/txt2html
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test/test_egor.rb
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test/test_egor_cli.rb
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test/test_enumerable_extensions.rb
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test/test_environment_feature.rb
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test/test_helper.rb
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test/test_nmatrix_extensions.rb
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website/index.html
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website/index.txt
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website/javascripts/rounded_corners_lite.inc.js
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website/stylesheets/screen.css
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website/template.html.erb
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data/PostInstall.txt
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data/README.rdoc
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= egor
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* http://egor.rubyforge.org
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== DESCRIPTION:
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egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
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== FEATURES/PROBLEMS:
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* No more segmentation fault
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* Full smoothing supported
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* Infinite number of environment features can be handled (in theory)
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== BASIC USAGE:
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$ egor -l TEMLIST-file -c classdef.dat
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or
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$ egor -f TEM-file -c classdef.dat
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== OPTIONS:
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--tem-file (-f) STRING: a tem file
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--tem-list (-l) STRING: a list for tem files
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--classdef (-c) STRING: a file for the defintion of environments (default: 'classdef.dat')
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--outfile (-o) STRING: output filename ("allmat.dat" if not specified)
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--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (not supported yet)
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--noweight: calculate substitution counts with no weights (default)
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--smooth (-s) INTEGER:
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0 for parial smoothing (default)
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1 for full smoothing
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--nosmooth: perform no smoothing operation
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--cys (-y) INTEGER: (!!!not implemented yet!!!)
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0 for using C and J only for structure
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1 for both structure and sequence (default)
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--output INTEGER:
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0 for raw counts (no-smoothing performed)
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1 for probabilities
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2 for log-odds (default)
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--scale INTEGER: log-odds matrices in 1/n bit units (default 3)
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--sigma DOUBLE: change the sigma value for smoothing (default 5)
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--add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/#classes)
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--penv: use environment-dependent frequencies for log-odds calculation (default false) (!!!not implemented yet!!!)
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--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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--verbose (-v) INTEGER
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0 for ERROR level (default)
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1 for WARN or above level
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2 for INFO or above level
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3 for DEBUG or above level
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--version: print version
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--help (-h): show help
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== REQUIREMENTS:
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* ruby 1.8.6 or above (http://www.ruby-lang.org)
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* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
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* narray (http://narray.rubyforge.org/)
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* facets (http://facets.rubyforge.org/)
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* bio (http://bioruby.open-bio.org/)
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== INSTALL:
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$ sudo gem install egor
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== LICENSE:
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(The MIT License)
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Copyright (c) 2008 Semin Lee
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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'Software'), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/Rakefile
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%w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
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require File.dirname(__FILE__) + '/lib/egor'
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# Generate all the Rake tasks
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# Run 'rake -T' to see list of generated tasks (from gem root directory)
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$hoe = Hoe.new('egor', Egor::VERSION) do |p|
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p.developer('Semin Lee', 'seminlee@gmail.com')
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p.changes = p.paragraphs_of("History.txt", 0..1).join("\n\n")
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p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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p.rubyforge_name = p.name # TODO this is default value
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p.extra_deps = [
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['narray','>= 0.5.9.5'],
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['bio', '>= 1.2.1'],
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['facets','>= 2.4.5'],
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['simple_memoize', '>= 1.0.0'],
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]
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p.extra_dev_deps = [
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['newgem', ">= #{::Newgem::VERSION}"]
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]
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p.clean_globs |= %w[**/.DS_Store tmp *.log]
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path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
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p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
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p.rsync_args = '-av --delete --ignore-errors'
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end
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require 'newgem/tasks' # load /tasks/*.rake
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Dir['tasks/**/*.rake'].each { |t| load t }
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# TODO - want other tests/tasks run by default? Add them to the list
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# task :default => [:spec, :features]
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data/bin/egor
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data/config/website.yml
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data/egor.gemspec
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = %q{egor}
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s.version = "0.0.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Semin Lee"]
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s.date = %q{2008-11-10}
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s.default_executable = %q{egor}
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s.description = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
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s.email = ["seminlee@gmail.com"]
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s.executables = ["egor"]
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
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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"]
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s.has_rdoc = true
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s.homepage = %q{http://egor.rubyforge.org}
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s.post_install_message = %q{PostInstall.txt}
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s.rdoc_options = ["--main", "README.rdoc"]
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s.require_paths = ["lib"]
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s.rubyforge_project = %q{egor}
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s.rubygems_version = %q{1.3.1}
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s.summary = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
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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"]
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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s.specification_version = 2
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
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s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
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s.add_runtime_dependency(%q<simple_memoize>, [">= 1.0.0"])
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s.add_development_dependency(%q<newgem>, [">= 1.0.7"])
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s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
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else
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
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s.add_dependency(%q<newgem>, [">= 1.0.7"])
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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end
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else
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
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s.add_dependency(%q<newgem>, [">= 1.0.7"])
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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end
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end
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