bio-protparam 0.1.0

data/test/helper.rb

@@ -0,0 +1,20 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'minitest/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'bio-protparam'
+require 'bio/db/embl/uniprot'
+
+class MiniTest::Unit::TestCase
+end
+
+MiniTest::Unit.autorun

data/test/test_bio-protparam.rb

@@ -0,0 +1,121 @@
+#
+# test/unit/bio/appl/test_protparam.rb - Unit test for
+# Bio::Protparam
+#
+#  Copyright::   Copyright (C) 2011
+#                Hiroyuki Nakamura <hiroyuki@1vq9.com>
+#  License::     The Ruby License
+#
+#  $Id:$
+#
+
+require 'helper'
+
+# libraries needed for the tests
+module Bio
+  class TestProtparam < MiniTest::Unit::TestCase
+    def setup
+      data = File.read(File.join('test', 'data', 'uniprot', 'p53_human.uniprot'))
+      uniprot = Bio::UniProt.new(data)
+      @obj = Bio::Protparam.new(uniprot.seq)
+    end
+
+    def test_num_neg
+      assert_equal(50, @obj.num_neg)
+    end
+
+    def test_num_pos
+      assert_equal(46, @obj.num_pos)
+    end
+
+    def test_amino_acid_number
+      assert_equal(393, @obj.amino_acid_number)
+    end
+
+    def test_total_atoms
+      assert_equal(6040, @obj.total_atoms)
+    end
+
+    def test_num_carbon
+      assert_equal(1898, @obj.num_carbon)
+    end
+
+    def test_num_hydrogen
+      assert_equal(2980, @obj.num_hydrogen)
+    end
+
+    def test_num_nitro
+      assert_equal(548, @obj.num_nitro)
+    end
+
+    def test_num_oxygen
+      assert_equal(592, @obj.num_oxygen)
+    end
+
+    def test_num_sulphur
+      assert_equal(22, @obj.num_sulphur)
+    end
+
+    def test_molecular_weight
+      assert_equal(43653.1, @obj.molecular_weight)
+    end
+
+    def test_theoretical_pI
+      assert_equal(6.33, @obj.theoretical_pI)
+    end
+
+    def test_half_life
+      assert_equal(1800, @obj.half_life(:mammalian))
+      assert_equal(1200, @obj.half_life(:yeast))
+      assert_equal(600, @obj.half_life(:ecoli))
+    end
+
+    def test_instability_index
+      assert_equal(73.59, @obj.instability_index)
+    end
+
+    def test_stability
+      assert_equal('unstable', @obj.stability)
+    end
+
+    def test_aliphatic_index
+      assert_equal(59.08, @obj.aliphatic_index)
+    end
+
+    def test_gravy
+      assert_equal(-0.756, @obj.gravy)
+    end
+
+    def test_aa_comp
+      correct_comp = {
+        :A =>  6.1,
+        :R =>  6.6,
+        :N =>  3.6,
+        :D =>  5.1,
+        :C =>  2.5,
+        :Q =>  3.8,
+        :E =>  7.6,
+        :G =>  5.9,
+        :H =>  3.1,
+        :I =>  2.0,
+        :L =>  8.1,
+        :K =>  5.1,
+        :M =>  3.1,
+        :F =>  2.8,
+        :P => 11.5,
+        :S =>  9.7,
+        :T =>  5.6,
+        :W =>  1.0,
+        :Y =>  2.3,
+        :V =>  4.6,
+        :O =>  0.0,
+        :U =>  0.0,
+        :B =>  0.0,
+        :Z =>  0.0,
+        :X =>  0.0,
+      }
+      assert_equal(correct_comp, @obj.aa_comp)
+    end
+  end
+
+end

metadata

@@ -0,0 +1,130 @@
+--- !ruby/object:Gem::Specification
+name: bio-protparam
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- hryk
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-12-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+description: Bio::Protparam has same interface and function as Bio::Tools::Protparam
+  class of BioPerl, except that it calculate parameters instead of throwing query
+  to Expasy protparam tool.
+email: hiroyuki@1vq9.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-protparam.rb
+- lib/bio/util/protparam.rb
+- test/data/uniprot/p53_human.uniprot
+- test/helper.rb
+- test/test_bio-protparam.rb
+homepage: http://github.com/hryk/bioruby-protparam
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 2302094890483272954
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: A Protparam compatible utility for BioRuby.
+test_files: []