bio-signalp 0.2.0 → 0.2.2

data/Gemfile

@@ -2,6 +2,7 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem "bio", ">= 1.4.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -9,6 +10,6 @@ group :development do
   gem "shoulda", ">= 0"
   gem "bundler", "~> 1.0.0"
   gem "jeweler", "~> 1.6.0"
-  gem "rcov", ">= 0"
   gem "bio", ">= 1.4.1"
+  gem "rdoc", "~> 3.12"
 end

data/Rakefile

@@ -32,14 +32,6 @@ Rake::TestTask.new(:test) do |test|
   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'
@@ -47,7 +39,7 @@ Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
   rdoc.rdoc_dir = 'rdoc'
-  rdoc.title = "bio-signalp #{version}"
+  rdoc.title = "bio-blah #{version}"
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.2

data/bin/signalp.rb

@@ -2,6 +2,9 @@
 
 require 'rubygems'
 require 'bio'
+
+# always load from the directory relative to the current script's directory
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), *%w[.. lib])
 require 'bio-signalp'
 
 # if this was not called as a module, run as a script.
@@ -71,9 +74,11 @@ if $0 == __FILE__
     ].join("\t")
   end
   
-  Bio::FlatFile.open(ARGV[0]).each do |seq|
+  Bio::FlatFile.open(ARGF).each do |seq|
     result = runner.calculate(seq.seq)
-    if options['s']
+    if result.nil?
+      $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
+    elsif options['s']
       puts [
       seq.entry_id,
       result.nn_D_prediction ? 'T' : 'F',

data/bio-signalp.gemspec

@@ -4,15 +4,14 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-signalp}
-  s.version = "0.2.0"
+  s.name = "bio-signalp"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ben J Woodcroft"]
-  s.date = %q{2012-01-06}
-  s.default_executable = %q{signalp.rb}
-  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.date = "2012-03-29"
+  s.description = "A wrapper for the signal peptide prediction algorith SignalP. Not very well supported, but seems to work for the author, at least."
+  s.email = "donttrustben near gmail.com"
   s.executables = ["signalp.rb"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -21,7 +20,6 @@ Gem::Specification.new do |s|
   s.files = [
     ".document",
     "Gemfile",
-    "Gemfile.lock",
     "LICENSE.txt",
     "README.rdoc",
     "Rakefile",
@@ -33,34 +31,37 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/test_bio-signalp.rb"
   ]
-  s.homepage = %q{http://github.com/wwood/bioruby-signalp}
+  s.homepage = "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}
+  s.rubygems_version = "1.8.17"
+  s.summary = "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_runtime_dependency(%q<bio>, [">= 1.4.1"])
       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"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
     else
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
       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"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
     end
   else
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
     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"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
   end
 end
 

data/lib/bio/appl/signalp.rb

@@ -9,7 +9,11 @@ module Bio
     class Wrapper
       # Given an amino acid sequence, return a SignalPResult
       # representing it taken from the file.
+      #
+      # Returns nil if the sequence is empty
       def calculate(sequence)
+        return nil if sequence.nil? or sequence == ''
+        
         command = 'signalp -trunc 70 -format short -t euk'
         Open3.popen3(command) do |stdin, stdout, stderr, wait_thr|
           stdin.puts '>wrapperSeq'

data/test/test_bio-signalp.rb

@@ -1,17 +1,57 @@
 require 'helper'
+require 'open3'
 
 class TestBioSignalp < Test::Unit::TestCase
   should "positive control" do
-    # Known to have a signal peptide
+  # Known to have a signal peptide
     acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
-    
+
     assert_equal true, Bio::SignalP::Wrapper.new.calculate(acp_sequence).signal?
   end
-  
+
   should "negative control" do
-    # Known to have a signal peptide
+  # Known to have a signal peptide
     non_signal_sequence = 'KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK'
-    
+
     assert_equal false, Bio::SignalP::Wrapper.new.calculate(non_signal_sequence).signal?
   end
 end
+
+class TestSignalPScript < Test::Unit::TestCase
+  command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
+  
+  should "positive control" do
+  # Known to have a signal peptide
+    acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+
+    Open3.popen3(command) do |stdin, stdout, stderr|
+      stdin.puts '>positive'
+      stdin.puts acp_sequence
+      stdin.close
+      
+      @result = stdout.readlines # convert to string?
+      @error  = stderr.readlines
+    end
+    assert_equal [">positive\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n"], @result
+    assert_equal [], @error
+  end
+  
+  should "return gracefully when empty sequences are given" do
+    acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+    
+    Open3.popen3(command) do |stdin, stdout, stderr|
+      stdin.puts '>positive'
+      stdin.puts acp_sequence
+      stdin.puts '>empty'
+      stdin.puts '>positive2'
+      stdin.puts acp_sequence
+      stdin.close
+      
+      @result = stdout.readlines # convert to string?
+      @error  = stderr.readlines
+    end
+    assert_equal [">positive\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n",
+    ">positive2\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n"], @result
+    assert_equal ["Unexpected empty sequence detected, ignoring: empty\n"], @error
+  end
+end

metadata

@@ -1,112 +1,94 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-signalp
-version: !ruby/object:Gem::Version 
-  hash: 23
+version: !ruby/object:Gem::Version
+  version: 0.2.2
   prerelease: 
-  segments: 
-  - 0
-  - 2
-  - 0
-  version: 0.2.0
 platform: ruby
-authors: 
+authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-01-06 00:00:00 +11:00
-default_executable: signalp.rb
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :development
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2012-03-29 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &68905280 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id001
-  name: shoulda
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :runtime
   prerelease: false
-- !ruby/object:Gem::Dependency 
+  version_requirements: *68905280
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &68904090 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *68904090
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &68962450 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
+      - !ruby/object:Gem::Version
         version: 1.0.0
-  version_requirements: *id002
-  name: bundler
-  prerelease: false
-- !ruby/object:Gem::Dependency 
   type: :development
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  prerelease: false
+  version_requirements: *68962450
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &68960950 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 15
-        segments: 
-        - 1
-        - 6
-        - 0
+      - !ruby/object:Gem::Version
         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 
+  version_requirements: *68960950
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &68958790 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 4
-        - 1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.1
-  version_requirements: *id005
-  name: bio
+  type: :development
+  prerelease: false
+  version_requirements: *68958790
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &68994130 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
   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.
+  version_requirements: *68994130
+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: 
+executables:
 - signalp.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
-- Gemfile.lock
 - LICENSE.txt
 - README.rdoc
 - Rakefile
@@ -117,39 +99,32 @@ files:
 - lib/bio/appl/signalp.rb
 - test/helper.rb
 - test/test_bio-signalp.rb
-has_rdoc: true
 homepage: http://github.com/wwood/bioruby-signalp
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -84068147
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.6.1
+rubygems_version: 1.8.17
 signing_key: 
 specification_version: 3
 summary: A wrapper for the signal peptide prediction algorith SignalP
 test_files: []
-

data/Gemfile.lock

@@ -1,22 +0,0 @@
-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