bio-wolf_psort_wrapper 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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+The biogem ```bio-wolf_psort_wrapper```
+=======================================
+
+A wrapper around the protein sub-cellular localisation program WoLF PSORT, so that it can be run locally. More information is about the underlying program is available from http://wolfpsort.org/aboutWoLF_PSORT.html.en and on the same site the executables required for this package to run are provided.
+
+```ruby
+    require 'bio-wolf_psort_wrapper'
+    wolf_psort_result = Bio::PSORT::WoLF_PSORT::Wrapper.new.run(
+      'MTQVPPVTFQQYGPVITTSAGNPVDDNQNSVTAGPYGPAILSNFHLIDKLAHFDRERIPE
+       RVVHAKGGGAFGYFEVTHDITRFCKAKLFEKIGKRTPVFARFSTVAGESGSADTRRDPRG
+       FALKFYTEEGNWDMVGNNTPIFFVRDAIKFPDFIHTQKRHPQTHLHDPNMVWDFFSLVPE
+       SVHQVTFLYTDRGTPDGFRHMNGYGSHTFKFINKDNEAFYVKWHFKTNQGIKNLNRQRAK
+       ELESEDPDYAVRDLFNAIAKREFPSWTFCIQVMPLKDAETYKWNVFDVTKVWPHGDYPLI
+       PVGRLVLDRNPENYFQDVEQAAFAPAHMVPGIEPSEDRMLQGRMFSYIDTHRHRLGANYH
+       QIPVNRPWNARGGDYSVRDGPMCVDGNKGSQLNYEPNSVDGFPKEDRNAAVSGTTTVSGT
+       VACHPQEHPNSDFEQPGNFYRTVLSEPEREALIGNIAEHLRQARRDIQERQVKIFYKCDP
+       EYGERVARAIGLPTAACYPAKM*'.gsub(/\s/,''),
+      'plant'
+    ) #=> Bio::PSORT::WoLF_PSORT::Report object
+    wolf_psort_result.score_hash #=> {'pero' => 8.0, 'nucl' => 2.0, 'mito' => 1.5, 'mito_plas' => 1.5, 'cyto_nucl' => 1.5}
+```
+
+Contributing to ```bio-wolf_psort_wrapper```
+--------------------------------------
+ 
+* 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-wolf_psort_wrapper"
+  gem.homepage = "http://github.com/wwood/bioruby-wolf_psort_wrapper"
+  gem.license = "MIT"
+  gem.summary = %Q{Enables the localisation predictor WoLF PSORT to be run locally}
+  gem.description = %Q{Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/}
+  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-wolf_psort_wrapper #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bio-wolf_psort_wrapper.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-wolf_psort_wrapper"
+  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 = "Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/"
+  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-wolf_psort_wrapper.gemspec",
+    "lib/bio-wolf_psort_wrapper.rb",
+    "lib/bio/appl/psort/wolf_psort_wrapper.rb",
+    "test/helper.rb",
+    "test/test_bio-wolf_psort_wrapper.rb"
+  ]
+  s.homepage = "http://github.com/wwood/bioruby-wolf_psort_wrapper"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.11"
+  s.summary = "Enables the localisation predictor WoLF PSORT to be run locally"
+
+  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-wolf_psort_wrapper.rb

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+require 'bio/appl/psort/wolf_psort_wrapper'

data/lib/bio/appl/psort/wolf_psort_wrapper.rb

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+require 'bio'
+
+module Bio
+  class PSORT
+    class WoLF_PSORT
+      class Wrapper
+        ORGANISM_TYPES = %w(plant animal fungi)
+        
+        SUMMARY_EXECUTABLE_NAME = 'runWolfPsortSummary'
+        
+        # Given an amino acid sequence as a String and an organism type (plasnt/animal/fungi) as a String,
+        # run a local version of WoLF_PSORT (which is assumed to be in the executable path) and
+        # return a parsed report. Return nil if something untoward happens. 
+        # 
+        # A known problem is that it doesn't
+        # work on sequences that are too short. For instance the sequence MRTLKTEVEKGFLSTMFVQELATPKG
+        # prints out an error on the command line:
+        # Modification of non-creatable array value attempted, subscript -1 at /home/ben/bioinfo/WoLFPSORT_package_v0.2/bin/psortModifiedForWolfFiles/psortModules/PsortFastaReader.pm line 440, <STDIN> line 1.
+        def run(amino_acid_sequence_string, organism_type)
+          fasta = ">wolf\n#{amino_acid_sequence_string}"
+          
+          output = Bio::Command.query_command([SUMMARY_EXECUTABLE_NAME, organism_type], fasta)
+          return nil if output == '' or output.nil? # happens when the sequence is too short
+          return Bio::PSORT::WoLF_PSORT::Report.parse_from_summary(organism_type, output.split("\n")[1])
+        end
+      end # class Wrapper
+      
+      # taken from http://wolfpsort.org/aboutWoLF_PSORT.html.en
+      LOCATIONS = [
+        'chlo',
+        'cyto',
+        'cysk',
+        'E.R.',
+        'extr',
+        'golg',
+        'lyso',
+        'mito',
+        'nucl',
+        'pero',
+        'plas',
+        'vacu' 
+      ]
+      ORGANISM_TYPES = [
+        'animal',
+        'plant',
+        'fungi'
+      ]
+      
+      class Report
+        # Name of the sequence that has been analyzed, according
+        # to WoLF_PSORT output
+        attr_accessor :name
+        
+        # plant, fungal or animal as a string
+        attr_accessor :organism_type
+        
+        # A hash of scores output, for example {'cyto' => 12}
+        # keys of the hash are strings representing localisations
+        # values of the hash are float output scores
+        attr_accessor :score_hash
+        
+        def initialize(name=nil, organism_type=nil, score_hash={})
+          @name = name
+          @organism_type = organism_type
+          @score_hash = score_hash
+        end
+      
+        # Given an output line from a the runWolfPsortSummary script,
+        # return a report with all the included information in it.
+        def self.parse_from_summary(organism_type, line)
+          line.strip!
+          return nil if line.match(/^\#/) #ignore the first comment line
+          
+          rep = self.new
+          rep.organism_type = organism_type
+          
+          line.split(', ').each_with_index do |fraction, index|
+            splits = fraction.split(' ')
+            if index == 0
+              raise ArgumentError, "invalid format\n[#{line}]" if splits.length != 3
+              rep.name = splits[0]
+              rep.score_hash[splits[1]] = splits[2].to_f
+            else
+              raise ArgumentError, "invalid format\n[#{line}]" if splits.length != 2
+              rep.score_hash[splits[0]] = splits[1].to_f
+            end
+          end
+          
+          return rep
+        end
+        
+        # Return the string of the highest predicted localisation
+        # recorded in the score hash
+        def highest_predicted_localization
+          @score_hash.max{ |a,b|
+            a[1] <=> b[1]
+          }[0]
+        end
+      end # class Report
+    end # class WoLF_PSORT
+  end # class PSORT
+end # module BioSORT

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-wolf_psort_wrapper'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-wolf_psort_wrapper.rb

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+require 'helper'
+
+module Bio
+  class PSORT
+    class WoLF_PSORT
+      class Report
+        # Equivalence to another WoLF_PSORT report. Written mainly 
+        # with testing in mind
+        def ==(another)
+          [:organism_type, :name, :score_hash].each do |attr|
+            return false if self.send(attr) != another.send(attr)
+          end
+          return true
+        end
+      end
+    end
+  end
+end  
+
+class WoLFPsortTest < Test::Unit::TestCase
+  def test_parse_summary_line_nil
+    assert_nil Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "# k used for kNN is: 14\n")
+  end
+  
+  def test_parse_summary_one_line
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'nucl' => 12, 'cyto' => 1, 'plas' => 1, 'cyto_plas' => 1}),
+    Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a nucl 12, cyto 1, plas 1, cyto_plas 1")
+  end
+  
+  def test_parse_summary_one_line_fungi
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}),
+    Bio::PSORT::WoLF_PSORT::Report.parse_from_summary('plant', "gcn5a cyto 17, nucl 9, cyto_pero 9")
+  end
+  
+  def test_amino_acid_sequence_prediction
+    # catalase pero 8, nucl 2, mito 1.5, cyto_nucl 1.5, mito_plas 1.5
+    assert_equal Bio::PSORT::WoLF_PSORT::Report.new('wolf', 'plant', {'pero' => 8.0, 'nucl' => 2.0, 'mito' => 1.5, 'mito_plas' => 1.5, 'cyto_nucl' => 1.5}),
+    Bio::PSORT::WoLF_PSORT::Wrapper.new.run(
+      'MTQVPPVTFQQYGPVITTSAGNPVDDNQNSVTAGPYGPAILSNFHLIDKLAHFDRERIPE
+RVVHAKGGGAFGYFEVTHDITRFCKAKLFEKIGKRTPVFARFSTVAGESGSADTRRDPRG
+FALKFYTEEGNWDMVGNNTPIFFVRDAIKFPDFIHTQKRHPQTHLHDPNMVWDFFSLVPE
+SVHQVTFLYTDRGTPDGFRHMNGYGSHTFKFINKDNEAFYVKWHFKTNQGIKNLNRQRAK
+ELESEDPDYAVRDLFNAIAKREFPSWTFCIQVMPLKDAETYKWNVFDVTKVWPHGDYPLI
+PVGRLVLDRNPENYFQDVEQAAFAPAHMVPGIEPSEDRMLQGRMFSYIDTHRHRLGANYH
+QIPVNRPWNARGGDYSVRDGPMCVDGNKGSQLNYEPNSVDGFPKEDRNAAVSGTTTVSGT
+VACHPQEHPNSDFEQPGNFYRTVLSEPEREALIGNIAEHLRQARRDIQERQVKIFYKCDP
+EYGERVARAIGLPTAACYPAKM*'.gsub(/\s/,''),
+      'plant'
+    )
+  end
+  
+  def test_too_small_amino_acid_sequence_prediction
+    # known problem - too short for WoLF_PSORT?
+    assert_nil Bio::PSORT::WoLF_PSORT::Wrapper.new.run('MRTLKTEVEKGFLSTMFVQELATPKG', 'animal')
+  end
+  
+  def test_highest_predicted_localization
+    assert_equal 'cyto', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 9}).highest_predicted_localization
+    assert_equal 'cyto_pero', Bio::PSORT::WoLF_PSORT::Report.new('gcn5a', 'plant', {'cyto' => 17, 'nucl' => 9, 'cyto_pero' => 90}).highest_predicted_localization
+  end
+end

metadata

@@ -0,0 +1,151 @@
+--- !ruby/object:Gem::Specification 
+name: bio-wolf_psort_wrapper
+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: Enables the localisation predictor WoLF PSORT to be run locally. The algorithm is available at http://wolfpsort.org/
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.mkd
+files: 
+- .document
+- Gemfile
+- LICENSE.txt
+- README.mkd
+- Rakefile
+- VERSION
+- bio-wolf_psort_wrapper.gemspec
+- lib/bio-wolf_psort_wrapper.rb
+- lib/bio/appl/psort/wolf_psort_wrapper.rb
+- test/helper.rb
+- test/test_bio-wolf_psort_wrapper.rb
+homepage: http://github.com/wwood/bioruby-wolf_psort_wrapper
+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: Enables the localisation predictor WoLF PSORT to be run locally
+test_files: []
+