bio-signalp 0.1.0

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", "~> 1.6.0"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.1)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.0)
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 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-signalp
+
+A wrapper for the signal peptide prediction algorithm SignalP.
+
+Using this bio-gem requires SignalP to be locally installed and configured correctly. http://www.cbs.dtu.dk/services/SignalP/ has instructions on how it may be downloaded. This gem requires that the signalp executable is available from the command line (i.e. running 'signalp' works at the command).
+
+Only compatible with Ruby 1.8 at this stage, because of the dependency on the rio gem. This might be replaced in the future with using BioRuby's Bio::Command class.
+
+This bio-gem is merely a software library, and does not (currently) include any scripts. An example script is freely available at https://github.com/wwood/bbbin/blob/master/signalp.rb
+
+== Contributing to bio-signalp
+ 
+* 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) 2011 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-signalp"
+  gem.homepage = "http://github.com/wwood/bioruby-signalp"
+  gem.license = "MIT"
+  gem.summary = %Q{A wrapper for the signal peptide prediction algorith SignalP}
+  gem.description = %Q{A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.}
+  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-signalp #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bio-signalp.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 = %q{bio-signalp}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Ben J Woodcroft"]
+  s.date = %q{2011-07-25}
+  s.description = %q{A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.}
+  s.email = %q{donttrustben near gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-signalp.gemspec",
+    "lib/bio-signalp.rb",
+    "lib/bio/appl/signalp.rb",
+    "test/helper.rb",
+    "test/test_bio-signalp.rb"
+  ]
+  s.homepage = %q{http://github.com/wwood/bioruby-signalp}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.6.1}
+  s.summary = %q{A wrapper for the signal peptide prediction algorith SignalP}
+
+  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>, ["~> 1.6.0"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.0"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+  end
+end
+

data/lib/bio-signalp.rb

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+# Please require your code below, respecting the bioruby directory tree. 
+# For instance, perhaps the only uncommented line in this file might 
+# be something like this:
+#
+#   require 'lib/bio/sequence/awesome_sequence_plugin_thingy'
+#
+# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
+# and put your plugin's code there. It is bad practice to write other code 
+# directly into this file, because doing so causes confusion if this biogem 
+# was ever to get merged into the main bioruby tree.
+require 'bio/appl/signalp'

data/lib/bio/appl/signalp.rb

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+# Methods to wrap around the signal peptide prediction program SignalP (version 3.0)
+require 'tempfile'
+require 'rubygems'
+require 'rio'
+
+# Wrapper around a locally installed SignalP program
+module Bio
+  class SignalP
+    class Wrapper      
+      # Given an amino acid sequence, return a SignalPResult
+      # representing it taken from the file.
+      def calculate(sequence)
+        Tempfile.open('signalpin') { |tempfilein|
+          # Write a fasta to the tempfile
+          tempfilein.puts '>wrapperSeq'
+          tempfilein.puts "#{sequence}"
+          tempfilein.close #required. Maybe because it doesn't flush otherwise?
+          
+          Tempfile.open('signalpout') {|out|
+            result = system("signalp -trunc 70 -format short -t euk #{tempfilein.path} >#{out.path}")
+            
+            if !result
+              raise Exception, "Running signalp program failed. $? is #{$!.inspect}"
+            end
+            line = rio(out.path)[2][0].strip
+            return Result.create_from_line(line)
+          }
+        }
+      end
+    end
+    
+    # The result of a SignalP program. Create using the output from
+    # -format short output and create_from_line()
+    class Result
+      @@nn_results = 
+      [:nn_Cmax, :nn_Cmax_position, :nn_Cmax_prediction, 
+      :nn_Ymax, :nn_Ymax_position, :nn_Ymax_prediction, 
+      :nn_Smax, :nn_Smax_position, :nn_Smax_prediction, 
+      :nn_Smean, :nn_Smean_prediction,
+      :nn_D, :nn_D_prediction]
+      @@hmm_results = [
+      :hmm_result, :hmm_Cmax, :hmm_Cmax_position, :hmm_Cmax_prediction, :hmm_Sprob, :hmm_Sprob_prediction]
+      
+      @@nn_results.each do |sym|
+        attr_accessor sym
+      end
+      @@hmm_results.each do |sym|
+        attr_accessor sym
+      end
+      
+      # Create a new SignalpResult using a line from the signal p 'short' output format,
+      # version 3.0
+      def self.create_from_line(line)
+        # e.g.
+        # # name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ?   # name      !  Cmax  pos ?  Sprob ?
+        # 526.m04658            0.734  19 Y  0.686  19 Y  0.933   6 Y  0.760 Y  0.723 Y 526.m04658  Q  0.037  19 N  0.004 N
+        matches = line.split(/[ \t]+/)
+        if matches.length != 21
+          raise Exception, "Bad SignalP Short Line Found (#{matches.length}): '#{line}'"
+        end
+        
+        i = 1
+        result = Result.new
+        result.nn_Cmax = matches[i].to_f; i += 1
+        result.nn_Cmax_position = matches[i].to_i; i += 1
+        result.nn_Cmax_prediction = to_bool matches[i]; i += 1
+        result.nn_Ymax = matches[i].to_f; i += 1
+        result.nn_Ymax_position = matches[i].to_i; i += 1
+        result.nn_Ymax_prediction = to_bool matches[i]; i += 1
+        result.nn_Smax = matches[i].to_f; i += 1
+        result.nn_Smax_position = matches[i].to_i; i += 1
+        result.nn_Smax_prediction = to_bool matches[i]; i += 1
+        result.nn_Smean = matches[i].to_f; i += 1
+        result.nn_Smean_prediction = to_bool matches[i]; i += 1
+        result.nn_D = matches[i].to_f; i += 1
+        result.nn_D_prediction = to_bool matches[i]; i += 1
+        
+        i+= 1
+        result.hmm_result = matches[i]; i += 1
+        result.hmm_Cmax = matches[i].to_f; i += 1
+        result.hmm_Cmax_position = matches[i].to_i; i += 1
+        result.hmm_Cmax_prediction = to_bool matches[i]; i += 1
+        result.hmm_Sprob = matches[i].to_f; i += 1
+        result.hmm_Sprob_prediction = to_bool matches[i]; i += 1
+        
+        return result
+      end
+      
+      def self.to_bool(string)
+        if string === 'Y'
+          return true
+        elsif string === 'N'
+          return false
+        else
+          return nil
+        end
+      end
+      
+      # Does it have a signal peptide? It can be this class (default), 
+      # or another class that responds to :nn_D_prediction and :hmm_Sprob_prediction
+      def signal?(clazz=self)
+        return (clazz.send(:nn_D_prediction) or clazz.send(:hmm_Sprob_prediction))
+      end
+      
+      def classical_signal_sequence?
+        return @nn_D_prediction
+      end
+      
+      def signal_anchor?
+        return @hmm_Sprob_prediction
+      end
+      
+      # Return an array of all the results. NN then HMM, as per SignalP short format
+      def all_results
+        all = []
+        
+        @@nn_results.each do |sym|
+          all.push self.send(sym)
+        end
+        
+        @@hmm_results.each do |sym|
+          all.push self.send(sym)
+        end
+        
+        return all
+      end
+      
+      # Return an array of symbols representing the names of the columns
+      def self.all_result_names
+        return [@@nn_results, @@hmm_results].flatten
+      end
+      
+      # Return the number of the residue after the cleavage site
+      # ie. the first residue of the mature protein
+      # Taken from the Y score, as it was decided this is the best prediction
+      def cleavage_site
+        @nn_Ymax_position
+      end
+      
+      # Given an amino acid sequence (as a string),
+      # chop it off and return the remnants
+      def cleave(sequence)
+        if signal?
+          return sequence[cleavage_site-1..sequence.length-1]
+        else
+          return sequence
+        end
+      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-signalp'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-signalp.rb

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+require 'helper'
+
+class TestBioSignalp < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: bio-signalp
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-07-25 00:00:00 +10:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  type: :development
+  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
+- !ruby/object:Gem::Dependency 
+  type: :development
+  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
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 15
+        segments: 
+        - 1
+        - 6
+        - 0
+        version: 1.6.0
+  version_requirements: *id003
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  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
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  version_requirements: *id005
+  name: bio
+  prerelease: false
+description: A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least.
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-signalp.gemspec
+- lib/bio-signalp.rb
+- lib/bio/appl/signalp.rb
+- test/helper.rb
+- test/test_bio-signalp.rb
+has_rdoc: true
+homepage: http://github.com/wwood/bioruby-signalp
+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: 1.6.1
+signing_key: 
+specification_version: 3
+summary: A wrapper for the signal peptide prediction algorith SignalP
+test_files: []
+