bio-plasmoap 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"
+
+gem 'bio-signalp', '>=0.2.0'
+
+# 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", ">= 1.4.1"
+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.rdoc

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+= bio-plasmoap
+
+Description goes here.
+
+== Contributing to bio-plasmoap
+ 
+* 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-plasmoap"
+  gem.homepage = "http://github.com/wwood/bioruby-plasmoap"
+  gem.license = "MIT"
+  gem.summary = %Q{Implementation of the PlasmoAP algorithm}
+  gem.description = %Q{The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.}
+  gem.email = "gmail.com after donttrustben"
+  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-plasmoap #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/plasmoap.rb

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+
+require 'bio-plasmoap'
+
+if $0 == __FILE__
+  runner = Bio::PlasmoAP.new
+  
+  # print out a list of proteins with yes/no answers
+  puts [
+    'Name',
+    'PlasmoAP Score',
+    'Apicoplast Targeted',
+    'Points'
+  ].join("\t")
+  
+  Bio::FlatFile.auto(ARGF).each do |seq|
+    result = runner.calculate_score(seq.seq)
+    to_print = [seq.definition, result.to_s]
+    if result.apicoplast_targeted?
+      to_print.push 1
+    else
+      to_print.push 0
+    end
+    to_print.push result.points
+    puts to_print.join("\t")
+  end
+end

data/lib/bio-plasmoap.rb

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+require 'bio/appl/plasmoap'

data/lib/bio/appl/plasmoap.rb

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+#!/usr/bin/ruby
+
+require 'bio'
+require 'bio-signalp'
+
+module Bio
+  # PlasmoAP is a program for predicting apicoplast targetting sequences
+  # in Plasmodium falciparum (the most fatal causative agent of malaria).
+  # This algorithm was designed based on what was outlined in the 
+  # PlasmoAP journal article 
+  #
+  # Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum.
+  # Foth BJ, Ralph SA, Tonkin CJ, Struck NS, Fraunholz M, Roos DS, Cowman AF, McFadden GI.
+  # Science. 2003 Jan 31;299(5607):705-8.
+  # PMID: 12560551
+  class PlasmoAP
+    # Calculate the PlasmoAP score for a sequence (a string of amino acids)
+    # sequence - the amino acids to test on
+    # has_signal_sequence - Define if it has a signal sequence or not. The default
+    # nil specifies that it should be worked out by SignalP.
+    def calculate_score(sequence, has_signal_sequence = nil, signalp_cleaved_sequence = nil)
+      # Only calculate signal sequence if it isn't already set by the parameter
+      if has_signal_sequence.nil?
+        # to_s means the sequence can be amino acid string or proper Bio::Sequence::AA object
+        signalp = Bio::SignalP::Wrapper.new.calculate(sequence.to_s)
+        has_signal_sequence = signalp.classical_signal_sequence?
+        
+        signalp_cleaved_sequence = signalp.cleave(sequence)
+      elsif signalp_cleaved_sequence.nil?
+        raise ArgumentError, "if the has_signal_sequence parameter is defined, then so must the signalp_cleaved_sequence be as well"
+      end
+      
+      return PlasmoAPResult.new(0) if !has_signal_sequence #Both set of rules need a signal peptide
+      
+      cleaved = Bio::Sequence::AA.new(signalp_cleaved_sequence)
+      
+      set1 = set1?(cleaved)
+      set2 = set2?(cleaved)
+      additional = additional?(cleaved)
+      
+      points = 0
+      points += 2 if set1
+      points += 2 if set2
+      points += 1 if additional
+      return PlasmoAPResult.new(points)
+    end
+    
+    private
+    
+    #      Set 1: a sequence is considered ‘positive’ if i) it starts with a signal peptide, ii) the 15
+    #amino acids following the predicted signal peptide do not contain more than 2 acidic
+    #residues, iii) the 80 amino acids following the predicted signal peptide cleavage site
+    #contain a stretch of 40 amino acids with a total of at least 9 asparagines and/or lysines,
+    #and iv) the asparagine/lysine-enriched region has a ratio of basic to acidic residues of at
+    #least 5 to 3.
+    def set1?(cleaved_amino_acids)
+      set1 = false
+      return false if cleaved_amino_acids.length <= 15
+      aa = Bio::Sequence::AA.new(cleaved_amino_acids[0..14])
+      if acidic_count(aa) <= 2 # ii)
+        aa = Bio::Sequence::AA.new(cleaved_amino_acids[15..15+80-1])
+        containing = nil
+        # iii) contain a stretch of 40 amino acids with a total of at least 9 asparagines and/or lysines
+        aa.window_search(40) do |window|
+          if !containing #only the first one is needed
+            comp = window.composition
+            if comp['N']+comp['K'] >= 9
+              containing = window
+            end
+          end
+        end
+        
+        if containing
+          if basic_count(containing).to_f / acidic_count(containing).to_f >= 5.0/3.0 # iv)
+            set1 = true
+          end
+        end
+      end
+      
+      return set1
+    end
+    
+    
+    #        Set 2: a sequence is considered ‘positive’ if it i) starts with a signal peptide, ii) if the 22
+    #amino acids following the predicted signal peptide cleavage site exhibit a ratio of basic to
+    #acidic residues of at least 10 to 7, iii) if the 80 amino acids following the predicted signal
+    #peptide cleavage site contain a stretch of 40 amino acids with a total of at least 9
+    #asparagines and/or lysines, and iv) if the asparagine/lysine-enriched region has a ratio of
+    #basic to acidic residues of at least 10 to 9.
+    def set2?(cleaved_amino_acids)
+      set2 = false
+      return false if cleaved_amino_acids.length <= 21
+      aa = Bio::Sequence::AA.new(cleaved_amino_acids[0..21])
+      if basic_count(aa).to_f / acidic_count(aa).to_f >= 10.0/7.0 #ii)
+        
+        # iii) if the 80 amino acids following the predicted signal
+        #peptide cleavage site contain a stretch of 40 amino acids with a total of at least 9
+        #asparagines and/or lysines
+        aa = Bio::Sequence::AA.new(cleaved_amino_acids[22..22+80-1])
+        containing = nil
+        aa.window_search(40) do |window|
+          if !containing #only the first one is needed
+            comp = window.composition
+            if comp['N']+comp['K'] >= 9
+              containing = window
+            end
+          end
+        end
+        
+        if containing
+          if basic_count(containing).to_f / acidic_count(containing).to_f >= 10.0/9.0 # iv)
+            set2 = true
+          end
+        end
+      end
+      return set2
+    end
+    
+    
+    # Additional point
+    # basic => nil for none, true for basic, false for acidic
+    def additional?(cleaved_amino_acids)
+      cleaved_amino_acids.window_search(1) do |aa|
+        if basic_count(aa) == 1
+          return true
+        elsif acidic_count(aa) == 1
+          return false
+        end
+      end
+      return nil
+    end
+    
+    private
+    ACIDIC_AMINO_ACIDS = %w(D E)
+    BASIC_AMINO_ACIDS = %w(H K R)
+    
+    # Return the number of bases considered acidic in this amino acid sequence in neutral conditions.
+    # Amino acids considered acidic are D and E. Input is a Bio::Sequence::AA object
+    def acidic_count(amino_acid_sequence)
+      count = 0
+      comp = amino_acid_sequence.composition
+      ACIDIC_AMINO_ACIDS.each do |acidic|
+        if comp[acidic]
+          count += comp[acidic]
+        end
+      end
+      return count
+    end
+
+    # Return the number of bases considered basic in this amino acid sequence in neutral conditions.
+    # Amino acids considered acidic are H, K and R. Input is a Bio::Sequence::AA object
+    def basic_count(amino_acid_sequence)
+      count = 0
+      comp = amino_acid_sequence.composition
+      BASIC_AMINO_ACIDS.each do |basic|
+        if comp[basic]
+          count += comp[basic]
+        end
+      end
+      return count
+    end
+
+
+  end # End class PlasmoAP
+  
+  
+  
+  class PlasmoAPResult
+    attr_reader :points
+    def initialize(points)
+      @points = points
+      raise Exception, "Bad PlasmoAP Score points: #{points}" if points < 0 or points > 5
+    end
+    
+    def to_s
+      case @points
+      when 0..2
+        return '-'
+      when 3
+        return '0'
+      when 4
+        return '+'
+      when 5
+        return '++'
+      end
+    end  
+    
+    def ==(another)
+      @points == another.points
+    end
+    
+    # '+' or '++' scores were taken as apicoplast targeted in the paper
+    # does this result pass that test?
+    def apicoplast_targeted?
+      @points >= 4
+    end
+    
+    alias_method :predicted?, :apicoplast_targeted?
+    alias_method :signal?, :apicoplast_targeted?
+  end
+end # End module Bio

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

data/test/test_bio-plasmoap.rb

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+require 'helper'
+
+class TestBioPlasmoap < Test::Unit::TestCase
+  def setup
+    # constructs are taken from the Science paper supplementary material.
+    # Constructs are made using ACP as the base amino acid sequence - the constructs deviate from that
+    signal = 'MKILLLCIIFLYYVNA'
+    transit = 'FKNTQKDGVSLQILKKKRSNQVNF'
+    rest = 'LNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    
+    @constructs = []
+    @names = []
+    
+    # base
+    @names.push 'base'
+    @constructs.push signal+transit+rest
+    
+    # no signal
+    @names.push 'no signal peptide'
+    @constructs.push 'M'+transit+rest
+    
+    # not transit
+    @names.push 'no transit peptide'
+    @constructs.push signal+rest
+    
+    # 2 A changes
+    @names.push '2 A changes'
+    myt = transit.clone
+    myt[1] = 'A'
+    myt[5] = 'A'
+    @constructs.push signal+myt+rest
+    
+    # 1 E change
+    @names.push '1 E change'
+    myt = transit.clone
+    myt[5] = 'E'
+    @constructs.push signal+myt+rest
+    
+    # another 1 E changed
+    @names.push 'another 1 E change'
+    myt = transit.clone
+    myt[1] = 'E'
+    @constructs.push signal+myt+rest
+    
+    
+    # 2 E changed
+    @names.push '2 E change'
+    myt = transit.clone
+    myt[1] = 'E'
+    myt[5] = 'E'
+    @constructs.push signal+myt+rest
+    
+    # 2 D changed
+    @names.push '2 D change'
+    myt = transit.clone
+    myt[1] = 'D'
+    myt[5] = 'D'
+    @constructs.push signal+myt+rest
+    
+    # 3 A changed
+    @names.push '3 A change'
+    myt = transit.clone
+    myt[10] = 'A'
+    myt[12] = 'A'
+    myt[13] = 'A'
+    @constructs.push signal+myt+rest
+    
+    @construct_points = [
+      5,
+      0,
+      1,
+      4,
+      5,
+      4,
+      0,
+      0,
+      5
+    ]
+    
+    @construct_strings = [
+      '++',
+      '-',
+      '-',
+      '+',
+      '++',
+      '+',
+      '-',
+      '-',
+      '++'
+    ]
+
+    @plasmoap = Bio::PlasmoAP.new
+  end
+  
+  def test_official_paper_constructs
+    @constructs.each_with_index do |construct, i|
+      obj = @plasmoap.calculate_score(construct)
+      assert_kind_of Bio::PlasmoAPResult, obj
+      assert_equal @construct_points[i], obj.points, "#{@names[i]}: #{i}: #{construct}"
+      assert_equal @construct_strings[i], obj.to_s, i
+    end
+  end
+  
+  def test_short
+    obj = @plasmoap.calculate_score('MMM')
+    assert_equal 0, obj.points
+  end
+  
+  def test_define_signal
+    signal = 'MKILLLCIIFLYYVNA'
+    transit = 'FKNTQKDGVSLQILKKKRSNQVNF'
+    rest = 'LNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    assert_raise ArgumentError do
+      @plasmoap.calculate_score(signal+transit+rest, false)
+    end
+    assert_equal 0, @plasmoap.calculate_score(signal+transit+rest, false, signal+transit+rest).points
+    assert_equal 5, @plasmoap.calculate_score(signal+transit+rest, true, transit+rest).points
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-plasmoap
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-01-06 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-signalp
+  requirement: &69055880 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *69055880
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &68875950 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *68875950
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &68874120 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *68874120
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &68872090 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *68872090
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &68870680 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *68870680
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &68869790 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *68869790
+description: The PlasmoAP algorithm (Foth and Ralph et. al. 2003) predicts apicoplast
+  transit peptides in Plasmodium falciparum. This is an implementation of that algorithm.
+email: gmail.com after donttrustben
+executables:
+- plasmoap.rb
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/plasmoap.rb
+- lib/bio-plasmoap.rb
+- lib/bio/appl/plasmoap.rb
+- test/helper.rb
+- test/test_bio-plasmoap.rb
+homepage: http://github.com/wwood/bioruby-plasmoap
+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: -824018541
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: Implementation of the PlasmoAP algorithm
+test_files: []