bio-exportpred 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.2"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J Woodcroft
+
+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/README.mkd

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+= bio-exportpred
+
+ExportPred is a computer program for predicting whether particular Plasmodium falciparum proteins are exported into the red blood cell cytosol during the intraerythrocytic stages. This biogem is a wrapper around the program, so that it can be interacted with programmatically.
+
+http://bioinf.wehi.edu.au/exportpred/
+
+Example usage:
+
+    positive_control = 'MAVSTYNNTRRNGLRYVLKRRTILSVFAVICMLSLNLSIFENNNNNYGFHCNKRHFKSLAEASPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETY'
+    result = Bio::ExportPred::Wrapper.new.calculate(positive) #=> Bio::ExportPred::Result object
+    assert_equal true, result.signal?
+    assert result.predicted_rle?
+
+== Contributing to bio-exportpred
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+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 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-exportpred"
+  gem.homepage = "http://github.com/wwood/bioruby-exportpred"
+  gem.license = "MIT"
+  gem.summary = %Q{Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins}
+  gem.description = %Q{Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-exportpred #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bio-exportpred.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-exportpred"
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Ben J Woodcroft"]
+  s.date = "2012-01-20"
+  s.description = "Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/"
+  s.email = "donttrustben near gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.mkd"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.mkd",
+    "Rakefile",
+    "VERSION",
+    "bio-exportpred.gemspec",
+    "lib/bio-exportpred.rb",
+    "lib/bio/appl/exportpred.rb",
+    "test/helper.rb",
+    "test/test_bio-exportpred.rb"
+  ]
+  s.homepage = "http://github.com/wwood/bioruby-exportpred"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.11"
+  s.summary = "Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+  end
+end
+

data/lib/bio-exportpred.rb

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+require 'bio/appl/exportpred'

data/lib/bio/appl/exportpred.rb

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+require 'open3'
+
+module Bio
+  class ExportPred
+    class Wrapper
+      # Use ExportPred called locally to predict whether a protein is exported or
+      # not.
+      # TODO: better doco here, explain options
+      def calculate(sequence, options={})
+        command = 'exportpred --input=-'
+        #--no-RLE and -r seem to fail when running exportpred on the command line, so here I'll just set the thresholds very high instead
+        command = "#{command} --KLD-threshold=99999" if options[:no_KLD]
+        command = "#{command} --RLE-threshold=99999" if options[:no_RLE]
+        
+        Open3.popen3(command) do |stdin, stdout, stderr, wait_thr|
+          stdin.puts '>wrapperSeq'
+          stdin.puts "#{sequence}"
+          stdin.close
+          
+          result = stdout.readlines
+          error = stderr.readlines
+          
+          unless error.length == 1
+            raise Exception, "There appears to be a problem while running ExportPred:\n#{error}"
+          end
+          parse_error = error[0].strip.match(/^(\d+) sequences read from stdin$/)
+          unless parse_error[1].to_i == 1
+            raise Exception, "There appears to be a problem while running ExportPred, unexpected output form: \n#{error}"
+          end
+          
+          # Error checking
+          unless [0,1].include?(result.length)
+            raise Exception, "Unexpected number of lines found in ExportPred output (#{result.length}:\n#{result}"
+          end
+          
+          return Result.create_from_line(result[0], options)
+        end
+      end
+    end
+    
+    class Result
+      @@all_result_names = [
+        :predicted_rle,
+        :predicted_kld,
+        :score
+      ]
+      @@all_result_names.each do |rn|
+        attr_accessor rn
+      end
+      
+      # Given the STDOUT from the ExportPred program, create a programmatically manipulatable Bio::ExportPred::Result object
+      #
+      # TODO: explain options={}
+      def self.create_from_line(line, options={})
+        result = Result.new
+        if !line or line == ''
+          result.predicted_rle = false unless options[:no_RLE]
+          result.predicted_kld = false unless options[:no_KLD]
+          return result
+        end
+        
+        # line is going to be something like
+        # metoo	RLE	6.44141	[a-met:M][a-leader:AVSTYNNTRRNGLRYVLKRR][a-hydrophobic:TILSVFAVICMLSL][a-spacer:NLSIFENNNNNYGFHCNKRH][a-RLE:FKSLAEA][a-tail:SPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETYKIPDEYKMRKFKFAHFEMQGYALKQEKFLLEYAFLSLNGKLCERKKFKEVLEYVKREWIEFRKSMFDVWKEKLASEFREHGEMLNQKRKLKQHELDRRAQREKMLEEHSRGIFAKGYLGEVESETIKKKTEHHENVNEDNVEKPKLQQHKVQPPKVQQQKVQPPKSQQQKVQPPKSQQQKVQPPKVQQQKVQPPKVQKPKLQNQKGQKQVSPKAKGNNQAKPTKGNKLKKN]
+        splits = line.split("\t")
+        raise Exception, "Badly parsed line: #{line}" if splits.length != 4
+        if splits[1] == 'RLE'
+          result.predicted_rle = true
+        elsif splits[1] = 'KLD'
+          result.predicted_kld = true
+        end
+        result.score = splits[2].to_f
+        return result
+      end
+      
+      def predicted?
+        @predicted_rle or @predicted_kld
+      end
+      alias_method :signal?, :predicted?
+      alias_method :predicted_rle?, :predicted_rle
+      alias_method :predicted_kld?, :predicted_kld
+      
+      def self.all_result_names
+        @@all_result_names
+      end
+    end
+  end
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-exportpred'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-exportpred.rb

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+require 'helper'
+
+class TestBioExportpred < Test::Unit::TestCase
+  def test_create_from_line
+    # test empty
+    line = ''
+    r = Bio::ExportPred::Result.create_from_line(line)
+    assert r
+    assert_kind_of Bio::ExportPred::Result, r
+    assert_equal false, r.predicted?
+    
+    line = 'metoo	RLE	6.44141	[a-met:M][a-leader:AVSTYNNTRRNGLRYVLKRR][a-hydrophobic:TILSVFAVICMLSL][a-spacer:NLSIFENNNNNYGFHCNKRH][a-RLE:FKSLAEA][a-tail:SPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETYKIPDEYKMRKFKFAHFEMQGYALKQEKFLLEYAFLSLNGKLCERKKFKEVLEYVKREWIEFRKSMFDVWKEKLASEFREHGEMLNQKRKLKQHELDRRAQREKMLEEHSRGIFAKGYLGEVESETIKKKTEHHENVNEDNVEKPKLQQHKVQPPKVQQQKVQPPKSQQQKVQPPKSQQQKVQPPKVQQQKVQPPKVQKPKLQNQKGQKQVSPKAKGNNQAKPTKGNKLKKN]'
+    r = Bio::ExportPred::Result.create_from_line(line)
+    assert r
+    assert_kind_of Bio::ExportPred::Result, r
+    assert r.predicted?
+    assert_equal 6.44141, r.score
+  end
+  
+  def test_create_from_line_options
+    # test empty
+    line = ''
+    r = Bio::ExportPred::Result.create_from_line(line, :no_RLE => true)
+    assert r
+    assert_kind_of Bio::ExportPred::Result, r
+    assert_equal false, r.predicted_kld
+    assert_equal nil, r.predicted_rle
+  end
+  
+  def test_wrapper_positive
+    positive = 'MAVSTYNNTRRNGLRYVLKRRTILSVFAVICMLSLNLSIFENNNNNYGFHCNKRHFKSLAEASPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETY'
+    result = Bio::ExportPred::Wrapper.new.calculate(positive)
+    assert_equal true, result.signal?
+    assert result.predicted_rle?
+  end
+  
+  def test_wrapper_negative
+    negative = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    assert_equal false, Bio::ExportPred::Wrapper.new.calculate(negative).signal?
+  end
+  
+  def test_no_rle
+    positive = 'MAVSTYNNTRRNGLRYVLKRRTILSVFAVICMLSLNLSIFENNNNNYGFHCNKRHFKSLAEASPEEHNNLRSHSTSDPKKNEEKSLSDEINKCDMKKYTAEEINEMINSSNEFINRNDMNIIFSYVHESEREKFKKVEENIFKFIQSIVETY'
+    result = Bio::ExportPred::Wrapper.new.calculate(positive, :no_RLE => true)
+    assert_equal nil, result.predicted_rle?
+    assert_equal false, result.signal?
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: bio-exportpred
+version: !ruby/object:Gem::Version 
+  hash: 29
+  prerelease: 
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-01-20 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id001
+  name: shoulda
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  version_requirements: *id002
+  name: bundler
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 6
+        - 4
+        version: 1.6.4
+  version_requirements: *id003
+  name: jeweler
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id004
+  name: rcov
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency 
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 1
+        - 4
+        - 2
+        version: 1.4.2
+  version_requirements: *id005
+  name: bio
+  prerelease: false
+  type: :development
+description: Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins. Requires local install of the program, which is available from http://bioinf.wehi.edu.au/exportpred/
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.mkd
+files: 
+- .document
+- Gemfile
+- LICENSE.txt
+- README.mkd
+- Rakefile
+- VERSION
+- bio-exportpred.gemspec
+- lib/bio-exportpred.rb
+- lib/bio/appl/exportpred.rb
+- test/helper.rb
+- test/test_bio-exportpred.rb
+homepage: http://github.com/wwood/bioruby-exportpred
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Wrapper around the ExportPred algorithm for predicting P. falciparum exported proteins
+test_files: []
+