bio-signalp 0.3.0 → 0.3.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 12404869c309796dffa4497c1021158943df36f5
+  data.tar.gz: 6a09580eb6dceebb59c6620a12f02cddef5e4143
+SHA512:
+  metadata.gz: 741919409e87ba018b96faae87609fe5ae779d780abb49fbce1cb0cd25c9169608347bfd6c68f2c46ff383d8bba4123113954f07c7db2942c7dd708707689acd
+  data.tar.gz: 7308fd484feaa9b7a38c2e2038052e2500b0a06c1100209e60e3f4469cdf03de14593c8912dd9938a7432d2ab4ee65a0cf28449e8ec53824e83e1a0d5c8250a1

data/.rspec

@@ -0,0 +1 @@
+--color

data/Gemfile

@@ -2,14 +2,14 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem "bio", ">= 1.4.1"
-gem "bio-logger"
+gem "bio", "~>1.4", ">= 1.4.1"
+gem "bio-logger", '~>1.0'
 
 # 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", ">= 1.6.0"
-  gem "rdoc", ">= 3.12"
+  gem "rspec", "~> 2.8"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", "~>1.0", ">= 1.0.21"
+  gem "rdoc", "~> 3.12"
 end

data/Rakefile

@@ -25,11 +25,10 @@ Jeweler::Tasks.new do |gem|
 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
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-task :default => :test
+task :default => :spec

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/bio-signalp.gemspec

@@ -2,14 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: bio-signalp 0.3.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-signalp"
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Ben J Woodcroft"]
-  s.date = "2012-08-18"
+  s.date = "2014-08-04"
   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"]
@@ -19,6 +21,7 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".rspec",
     "Gemfile",
     "LICENSE.txt",
     "README.md",
@@ -30,40 +33,39 @@ Gem::Specification.new do |s|
     "lib/bio/appl/common.rb",
     "lib/bio/appl/signalp3.rb",
     "lib/bio/appl/signalp4.rb",
-    "test/helper.rb",
-    "test/test_bio-signalp.rb"
+    "spec/bio-signalp_spec.rb",
+    "spec/spec_helper.rb"
   ]
   s.homepage = "http://github.com/wwood/bioruby-signalp"
   s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.24"
+  s.rubygems_version = "2.2.2"
   s.summary = "A wrapper for the signal peptide prediction algorith SignalP"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_runtime_dependency(%q<bio-logger>, [">= 0"])
-      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<rdoc>, [">= 3.12"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1", "~> 1.4"])
+      s.add_runtime_dependency(%q<bio-logger>, ["~> 1.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.8"])
+      s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
+      s.add_development_dependency(%q<bundler>, [">= 1.0.21", "~> 1.0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
     else
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<bio-logger>, [">= 0"])
-      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<rdoc>, [">= 3.12"])
+      s.add_dependency(%q<bio>, [">= 1.4.1", "~> 1.4"])
+      s.add_dependency(%q<bio-logger>, ["~> 1.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.8"])
+      s.add_dependency(%q<jeweler>, ["~> 2.0"])
+      s.add_dependency(%q<bundler>, [">= 1.0.21", "~> 1.0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
     end
   else
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<bio-logger>, [">= 0"])
-    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<rdoc>, [">= 3.12"])
+    s.add_dependency(%q<bio>, [">= 1.4.1", "~> 1.4"])
+    s.add_dependency(%q<bio-logger>, ["~> 1.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.8"])
+    s.add_dependency(%q<jeweler>, ["~> 2.0"])
+    s.add_dependency(%q<bundler>, [">= 1.0.21", "~> 1.0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
   end
 end
 

data/lib/bio/appl/common.rb

@@ -2,12 +2,12 @@ module Bio
   module SignalP
     NUM_FIELDS_IN_VERSION3_SHORT_OUTPUT = 21
     NUM_FIELDS_IN_VERSION4_SHORT_OUTPUT = 12
-    
+
     class Wrapper
       def log
         log = Bio::Log::LoggerPlus['bio-signalp']
       end
-      
+
       # Given an amino acid sequence, return a SignalP Result
       # representing it taken from the file. The version of SignalP used
       # is auto-detected (versions 3 and 4 are supported)
@@ -18,35 +18,35 @@ module Bio
       # Returns nil if the sequence is empty
       def calculate(sequence, options={})
         return nil if sequence.nil? or sequence == ''
-        
+
         default_options = {
           :binary_path => 'signalp'
         }
         options = default_options.merge options
         raise "Unexpected option parameters passed in #{options.inspect}" unless options.length == default_options.length
         options[:binary_path] ||= default_options[:binary_path] #in case nil is passed here
-        
+
         # This command needs to work with all versions of SignalP (currently v3 and v4)
         command = "#{options[:binary_path]} -f short -t euk"
         log.debug "Running signalp command: #{command}" if log.debug?
         Open3.popen3(command) do |stdin, stdout, stderr, wait_thr|
           stdin.puts '>wrapperSeq'
-          stdin.puts "#{sequence}"
+          stdin.puts "#{sequence[0..500]}" #Only give the first 500 amino acids because v3 fails on massive aaseqs
           stdin.close
-          
+
           result = stdout.readlines
           error = stderr.readlines
-          
+
           unless error.empty?
             raise Exception, "There appears to be a problem while running signalp:\n#{error}"
           end
-          
+
           # Error checking
           num_expected_result_lines = 3
           unless result.length == num_expected_result_lines
             raise Exception, "Unexpected number of lines found in SignalP output (#{result.length}, expected #{num_expected_result_lines}):\n#{result}"
           end
-          
+
           splits = result[2].strip.split(/[ \t]+/)
           if splits.length == NUM_FIELDS_IN_VERSION3_SHORT_OUTPUT
             # SignalP 3 detected, use that
@@ -63,7 +63,7 @@ module Bio
         end
       end
     end
-    
+
     # A module for methods common to different SignalP version Result classes.
     module Common
       # Given an amino acid sequence (as a string),
@@ -76,7 +76,7 @@ module Bio
           return sequence
         end
       end
-      
+
       # Simple method: 'Y' => true, 'N' => false, else nil
       def to_bool(string)
         if string === 'Y'
@@ -89,4 +89,4 @@ module Bio
       end
     end
   end
-end
+end

data/spec/bio-signalp_spec.rb

@@ -0,0 +1,162 @@
+require 'spec_helper'
+require 'open3'
+
+SIGNALP3_PATH = File.join(ENV['HOME'],'bioinfo','signalp-3.0','signalp')
+SIGNALP4_PATH = File.join(ENV['HOME'],'bioinfo','signalp-4.0','signalp')
+SIGNALP_BINARIES = [
+  SIGNALP3_PATH,
+  SIGNALP4_PATH,
+]
+
+describe 'bio-signalp library' do
+  def setup
+    log_name = 'bio-signalp'
+    Bio::Log::CLI.logger('stderr')
+    #Bio::Log::CLI.configure(log_name) # when commented out no debug is printed out
+  end
+
+  it "positive control" do
+  # Known to have a signal peptide
+    acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+
+    Bio::SignalP::Wrapper.new.calculate(acp_sequence).signal?.should == true
+  end
+
+  it "negative control" do
+  # Known to have a signal peptide
+    non_signal_sequence = 'KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK'
+
+    Bio::SignalP::Wrapper.new.calculate(non_signal_sequence).signal?.should == false
+  end
+
+  it 'work with different SignalP versions, this test is specific to Ben\'s machines probably' do
+    binaries = {
+      SIGNALP_BINARIES[0] => Bio::SignalP::Version3::Result,
+      SIGNALP_BINARIES[1] => Bio::SignalP::Version4::Result,
+    }
+    binaries.each do |binary, clazz|
+      acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+      positive_result = Bio::SignalP::Wrapper.new.calculate(acp_sequence, :binary_path => binary)
+      positive_result.signal?.should == true
+      positive_result.should be_kind_of(clazz)
+      positive_result.cleavage_site.should == 17
+      positive_result.cleave(acp_sequence).should == 'FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+      non_signal_sequence = 'KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK'
+      Bio::SignalP::Wrapper.new.calculate(non_signal_sequence, :binary_path => binary).signal?.should == false
+    end
+  end
+
+  it 'give different predictions for v3 and v4' do
+    different = <<EOF
+MMKGMVEAAVKWMKAGLPLRILKLVLYAKVIDGDLQGHSLRRFSEVLKTFTELKERYEMQ
+LLLPKAVPLEFDVYLSFSEEDKEVAKVIREKLSGAKDGVRIYDSSHQGINKDTVFQEDMY
+SIMMKSARVVTVLSPNYLRNKACIEQYNIALCCNRRALRDMLAPIYVDSVEMMPTYMGLV
+QYVDCRPHDPSKIGEACSQLTVSLSVTFHTELRVAEFDPLRYDVFLSYSHRDTEKANRFV
+EMLQKLAPDLKLFFDVQELKTGKSWQRTLYHSIDGSRCMLALISEPYLKSAVCQEEFALA
+QAKHCAKGKQHLQLISICLDDLDTIQPEFTHIPMVKGTPDVFDDMVKTVCPAVIQWLNGE
+RVDQTETIKTLFDDQNITTLSADAEMEKFRQSHFQKEFGTQDSLISSKSPFPPKLSDILP
+EPGKEVKDKRPKSASDCDLIFSYHSDDEKYVSFIVKILQLNAPSLKVKAVCSDENKLSAF
+ERAHCIVPVLSPNYLESPECVEEFHIAIWRQRISNPEAGALLPICVHTLPQKPTYFHLVQ
+SAVSMTDGIWAQLSGQHNFGLPQKIVDFSLAAGKTPLSQVDMLALYMAAYYILKRFAKAR
+SCKEVEFSMKPALFNIMKLQEQIKQLTQPDYTDQLCKTLLEIHFNDIPDSWREGGHYLRP
+KEPEDTTPAIMAPVEGASDSQTHNALNERTQDSSGKDKSEVQGEKAQRSASEGVSHDTVQ
+QMDQDHDLKAAQGQDTAEGQDAAEGQDSEGGQDSEGGWDSDGGRDSVGNKTDAEKITGNH
+GDEGGDGQVGGSEESKEKTEDEDEDISKRNRAPRSVACVCL
+EOF
+    Bio::SignalP::Wrapper.new.calculate(different, :binary_path => SIGNALP3_PATH).signal?.should == true
+    Bio::SignalP::Wrapper.new.calculate(different, :binary_path => SIGNALP4_PATH).signal?.should == false
+  end
+
+  it 'work when given a very large sequence for signalp 3' do
+    big_seq = 'MTPEMPNPLDPSLAFNMAPGDVQLATGPQQPAAVFASPLQDAMVKPTQAQIPLHHENDKGNQELGPDRDQVYHIRTTSFKSLGCWKDTWDRAIPLMERKHPLLYEDDYKSRTNALMKCAEAALDNNFSIFSVQNGGQCFSGKDADRTYMKYGVSRTCKACQTAIDLVFLIDGSASVERYGIGNFRRLIDFVRDVVIGFRVSRGNTRVGAIVFGTKPYVLFGFNKYTNNGALFNKLNQGVQYPKSGSRIGRALLMAQNRLFRKNSRRSRTTKVVVVITDGSSMDDVAGPSNALKALGVRIYCVGVGRYINGRQLDILASPPRKNHIFTADWKHLSVIVNDLRNAVCLGTGGNLVAATHRVCLCPYTHPTEKPSTKPPLRPGFPRVVALYPLSKRTKGKDISGNRNPNGELSGVYPAPGPDGLPDGSYYFSGRKTSYIQFPNDGKLDSYYSLTMLAWIYPEGSGPIFHFFPGGVRFWVVRPNTLIITFVRRTGRPAQQLISHKLIPKRWNYVGASYDERTGIATLWRDSRPIESVYIGRIRLATNRPVRMGALPRDLRYFRGRISCMQVYSVPLSGPEIKRAEKVCFRTVRMGAKIGDRRCFRGWITCMQVYDQPLPLRLIRIAKRLCFKAYPTPSPSTTPTILRPGKLCRARIDLGLLVDGTNNRYRFKKILNVVNQLIRYFDISRVYTRIGVIAYSSSSIPYFNFKRFARKYDVLGAVRKISFPQGVSYTGRALRFAGRYLFPGTRRTYARSKVLVVFTGAQSKDSVARPAQMLKRSGVEIFAVGTGSWSSRSYLESIAYDRYHVFNTDSRLGLKTVLDRLVAKICVATPIGKPTTATRPTTTKSTTPTQRIVPPPAMAIYPLNGIDRGKDIGPFKNPTAKLENVVSKSGPDGLPAGSYQLQGFANSYISFPNTGRLDTQNSITIICWLFPESAGPVFHYKPQGVGVNLRMISRKVIRAEFVSRDGRITKRISKRIRSRVWNYIAGTYDYNTGLATIWLDAIPITQRNIGRMRLATNYPAVSGRKSGDPRHFRGRIACVQIYNVALNSYQIRKLKRLCFRARPPYTPTPTRPSLPRIVAIYPLDEQNKGRDISQNRNPTGQLLGVRPAPGPDGWPNTATEFFGNENSYIEFPNSGKLDTINSITVLAWVFHSGVSGPIFNFNVGPGRGVQFWMMGPRKLYARFVRRDGLLTTPLVTHGATVPYKAWAYLGTTYDGNTGVASLYVNNRPVVRTNIGRIRLATNKPVRMGAKKGDRRYFRGRVSCVQVYSLALNRRQISRAAKRCFKIVCKPVVDLGFLIDGSGSIEYHGRGNFKLMLNFIKSMVASLPISRTQSRIGAVLFSDKPIPLFRFGQLNSVTHVIQAIDSIRYPRGGTYIGRALSFIRRYLFSGRRKSNRKRILILLTDGLSKDGVRREASLLKKRDVEVFAVGIVPLPSSLAVYALDGYRRGKDISGSNNPTASLIGTGTAPGPDGRRDGSIKFYGRRNSYVRITNSGRLDAQFSITIIVWMFHDGVNGPFVHYNPQGLGVELAMTGRREIVARFVKRSSSYSVPLKSRQIKYRAWNYVATTFEQRTGLAKLYINSRQVAYKTVGRMRLATNYPLRLGAREDDRRYFRGRLFCLQIYSMPLTGRQIEAAKRRCFLPTPTPTKPTPTRVPPPPPPRVCRARIDLGFLVDASSSRLNSGAIRQFIKETVRRFEVSSTLVRIGVVTYSYSPKLLVGFGRSYSRPQIYRLVDRMQVKGYGGRYLGKALDYTRRYLFSATPRCGRRRVLMVLTTGESRDAVRPYALKMFGSGVEVYAIGIGRVRRKSLFQIATRYRLAFRVNAGRLIYLTRKIKDRICSYPGKAVAVYPFNSASYGRDVSKFKNPTAQLVGLSFIKGPDGHQQGAYFFPGKGRRGVRSSYALIPNNGCLDTRYSITITCWVYPEAPGPILHFNPNGWGLHLWLTRTDELFFRVIPRQGSRQKAKPVISRSVKPFKWNYISGTYDHLTGLATLWVDGVPCAQRNVGKFPLGLATNYPAVVGRRPGDNRVFRGRITCLQVYNVALTRPQIIARKEKCFRRVPLPRTLAVYPLDLRRRGQDISRRRNPSARIGDIKYGRGPDGRQTGSTVFSGRRGSYVEIPNRGNLDARYSITILIWLFHLGTSGPIVHFNPNGYGVHMWMTSQRELFVRFVRRGGAMTTPIRSKRLTYKAWNYVGASYDDRSGIGTLWINSRSVARRNLGKIRLSTNYPIRLGATKRSRTYFRGKLFCFQIYSVPLTQKQVFEAKKRCFLPGPTPTKPTPTRKPTPPPRMILTRGAVATYTFSRASRGRDISQYKNPTARLVGISYTRGPDRNPQGAYYFPGVKRIRGRTITSYVLLPNNGCLDTRFSFTVLFWLFGESPGTLVHFNPNGAGVEVRLSRLTQLYFHVVPRGRSGRSVRPLIGNGVRPRTWNYIAATYDIRTGLATFYVNDFPVAQRNVGKFRSGVATNYPILIGKSPGNRRVFRGRLACLQIFNVALSRSKIVSLKKRCFQTRRTTRGRKRTLLVITDGVSSDRVKQPSLSLKRNGVQIFALGVGSGFRRSQLQLIATSPADVFTAGFGRLGTLVKAIKEKICLPSIPTPTRPPRAVALYPLNSRTQGRDIGPRKNKPARLTGVRLAPGPDGFPRGSIYFSGWRGSFAYFPNNGGIDTRNAITILVWIKPEKDGPIFHYNTQGSGVSVRIVRKKVLYVKFVRRSGKGSYVLKTVGLRPRVWNYFGVTYDGRTGLATIWRESTPLAQGNIGRGLRLATNYPAIMGSRPGSNTYFRGSIACLQVFDLALNGLRIRKRRNVCFRGAPPPVPSPPGTKDITNNNQPGIPSNVRPAPGPDGRKKGSTLFTGSINSYIEFPNNGKLDTRRSTTILAWVFHSGKSGPIFNYDRRGFGVHLWMVGPRVLFVRFVRRSKRRTASVATYAKKPNYRAWNYIGASYDYSSGVATLWLNSEPVARQSIGRFDLATDYPVRMGARVGDKNAFRGKISCLQVYSVALTAKQIRGARKRCFKKVIEPTHTMCGTPVDLGFLIDGSGSIEYQGKGNFVRILNFVKSIISFFEVSRGKSRVGCVLFSSRTIPIFGFRRYSSKAKILKAIGRIRFPRGGTKIGKALDFTRDYLFKGRSTRGKKRILTLITDGISMDKVGPAASRLKAAGVEVFTIGLGRKFKLSQLYQVATDPYHVLTASFSSMMTLIMKLKNQICQRGGPPITTPPPTTRPSRLPRIPTTSPSGKPTTRAVVTYAFRTKPIISFARSYTLSRVYSALRGMQVLGGRRRLGSALYSVKQNLFAAKPLCGQRRVLIVVNGGESVDRVRKPAQTLEGAGVEIFVVGVDGVGRRTASQLVTDRAHLFMVRFARLNTIIKTLKDRICYSPAIVRRGAVAVYPFTLTSKNRDISGYVNPPATFVGRLKYSFGPNKHPQGALYFSGERNTYVLIPNNGCLDTRFSITIAFWVYPLQPGSLVHFNPDGSGMDVSIVMPFKVSVRLISRSGKSVISLEKRIPKDKWTYLTVTSDHKTRLATLWFDSIPFDQRRIDGFRYGFATNYPISIGGTRRGTRRFKGKISCLQIYNYALTKAQIYSKMTRCFSSGVYSELPFLLVDDATHHFRNPLGCLLCALFSSIFGVEVFIARSYFSIYTERLPSTLAVYPLDRKRKGKDISSSRNPSADLNSVGYNEGPDGRRFGSVEFSGQSNSYAIIPNNGNLDARYSITVLVHVFYQGGSGSFFNYNPKEKGLLLRMISATKLEVEIIDRKRRTSIKVQTPGRVFQREAWNYVGMTYSERRQLVSIWVNLKLVATKRVGKVELDTGHPIRLSGYKNSRGYFRGRLFCLQLYSVALTGEKIKEAMKKCFLKGPITIPTSPSLPTPAPRVCTARIDLGFVLETSSTAMRNGNRYYTRFLRKIVQVFTITKDTTRVGIVTYATRTYGNIAFTGSYTRRLVYSAISRIRQLGRGRRLGKALTYARTYLFKGKPQCGRRRILIVLTAGGSTDKVRQARQGLQKAGVEIFVVGVGGVSRRTLMQVATDRQHIFKIQFAQLHTIVNTLKDIMCYSPVRTPSPPIPSTPPVKLPRTLAVYPFDKKRGRTDISRGKNPPAVFGKVVAYGEGPDSRKDGSFQFSGRKDSYIVIPNDGRLDAKYSITVLIWAFPVSRSGVILTYNPAGKGFQLRIIYPQRLQVILVERTRRTTITINTPRPVIQYKAWNYIGVTYSESAQKITIYVDSKAVATKTIGKVQLNTRYPIRLGGRGGVILRRGAIAVYQFTGVSRNRDISGYLNPPAMFYGVSYLTGPDKNPRGALYFKGKRGSYVSIPNNGCLDTKYSITIIFWVYPRSLGPLIHFNPNGRGVDLSIENPFTLYARFVPRSGKFVRPVRKTIPQRQWSYIAASYDSTTGLASLFRNGFLVAQTRIGRFRFGLATNYPILIGRRPRDRRYFNGEISCLQIYNYALDGVQIRSKMTSCFTPESLPSTLAVYPLDEERQGRDISKEKNPTATLVRVSFGEGPFGRETGSTQFDKRSSYVKISNNGKLDAKYSITVLIWVYMERWGNILKYGPTGKGFEVSIISQRKLQVEIVERTRRTRFTIITPRPVIEPKVWRYIGVTYSERAERMIIWVNSKAVAFKIIRKVQLDTKYQIRLGGQDGKGQYFRGRLFCLQIYSVALLEKQIRYAGKNVSLKVHPLHVRLQPHDQRDLHQIDLGFLIDATTTVLRSRSQNYQQVVKFLREILKYFKVSRTATRIGIVTYASRIRTVMSFSRSYRRREVYNAILGIRELGGRRQLGKALTYARTNLFRGRPQCGRRRILMVLTAGGSVDQVQGSSLSLLASGVEIFMIGVGRVSRQTLLQVTTDRRHVFVIGFTQLYTIAKTLKDNSCYNPVIRRRGAVAVYQFTGTSGNRDVSRYVNPPARFEGVYFYRGPDNDARGSLSFRGTRNSFVLIPNNGCLDTRYSITILFWVYPVSIGPLVHFNPNGLGVHVWIIKPFTIYCRVMPRSGKSVKPLYYKIKPRQWSYIGLTYNHKTGVATLWVFSIPVVQHVIGRFRLGLATNYPIYIGQKPNDKRRFRGRISCLQIYNYAMDGVEMRSKMTRCYKPDKIPKALAVYPLDDKRDGSDISSNQNSPAKLYNIKYAEGPDMRKKGSSQFDGQSRTYVFIPNTGKLDTKYSITVLVWMYPEGRRGFVFKYSSNKFVVRVIRPRVLQVEIRGRLRRTTITVNTPGNVIRYKAWNYIGVTCDRRSNVVTIWVNSKPVAKTGLRKVQLDTRKDITLGGGNFRGRLFCLQVYSVPLSQRQIEGARKKCFLKEPNITLPPPITTPTPAPSVCTARIDLGFIVEATSSAMRSQSRQIKQFLRETVRRFTISTTAARIGLITYASRAVGLLRFTGAYTRRLVNNAINRIRELSGQRRLGRALYYAKRYLFVGNPQCGRRRILIILTAGRSIDRVLQPAQSLKGAGVEIFSVDVGRVGSHTLFKVATDRHHVFRVAFAKLFTILRPLKERICYSPVVIRHGAVAIYPLTSASKNRDTSPYKNPPATFFNVEFSYGPDNHQKGALSFKGRRNSYVFIPNNGCLDTRYSMTIILWIYPVGLGPVIHFNPKGRGVDIDIGSGFRLYARFRSRSGNFVKVLYKKIKPRQWNYVAASYDYRLGIATLWRDSRPSVQRRIGRFGLATKYSIVIGQKTGYTRYFQGKITCLQIYNFAMTGEQIRSKKKWCFRQVPLVPTTPVFPKVPTGKVPGVLALYPLDYKRGGSDISSNQNSPAKLYNIKYAEGPDMRKKGSSQFDGQSRTTHNHPTYPADANPCTEICSVPVDLGFLIDATTTVMRSGSRYYRQFLREIVKRLIVSRSRTRVAVYTFASRTSRNIGFAGSYSRGQVYSAVNGIRQLSGARYLGKALRDTKTYMFRGKPQCGRRRILIVLTGGGSVDRARGPALSLLGSGVEIFVIGVGRISSQSLIHVTTDRQHVFVVGYSRLYSIVQTLMDKICCQSVIRRRRAVAVYQFTGASNNRDVSGSVNPPAIFVGVYYSVGPDKRPRGALSFRGTSKSVRPVSKTIPSNRWSYIAASYDYSSGLASLWSYNTLVDQRRIGRFRLGLATNYPIYIGRKPGDRRRFRGEISCLQIYNFAMTGPQIRSKMARCYNPATGPTTRPITLPYTPTVPMPPSLAVYPLDKKRGGIDITGRNPSARFKGTVFGDGPDGRKQGSTKLSGRSNSYVLIPNTGKLDPRYSITVLIWVYPIRSRGIVLTYNPNRKGFQLRIISPRKLLLEMVERTRRTTIRVSTPRPVIERKIWNYIGVTYSMKSKRVTFWVNSKAIATKVIGKVELDTRGSIRLGGYRGSRDFFKGRLSCLQVYSVELTSRQIEEAKKRCFLKVPITVPIPSPSPTRPPRVCTARVDLGFLIDATSASLRSNNRNYMEQFMQQLLRRFVISGRSTRVGLLTFSARTHRLLGFAGSYTTKGLGPLVHFNPFGSGVQISLVSPFRLSARFVPRSGKWVNAVYANITPRRWYYVATTFDHTNGVVSIFVNNALLSQRRIGPFRFGLATNKPVVIGGKPGSRRSFRGKISCLQVYNYPMNLLQIRSKEKLCFRAVLTPSPTITTPYTGSKPPIPSPSSKQPPAYPAFPFNRYNSKASVVRAVDRVRFPYGGTRTGNALRFTSGYLFPRGRIRGRKPFLVIITDGKSQDGVAAPAASLKRKGVDIFALGYGTKFRRLDLQQMASSPSYVMTASFGKISAILAAVKKKACQPFVPPTTPATVPACSLSIDVGLVLDSSARVGRWGFRQIKRFARLIARSFTISQKYGRVGVIVYGSYPRVEFGLNRYFNARYVDRTIERLRFIGGLRRTGKALEMALSGLFRGSRKKRVLVFVTNGPAADGIRLPSLRIHQSGIETFAIGIGSRSSHRELSAIATNARHTYMVTFRTLKSIVKSIVRKACKGFPEPVAIYTLHRKGGTVDISPGKNVPGQSSNVRYAPGPYGQSYKSTEFLGNRNSYIRFPNNGKLSVKHSITLLAWVYPMKPGPIFEYLRGVKFWCFRSDSLYVHFARRDRRRTRVLRKRRLRPYRWNYVGATYDQRTGIATLWLNSSPILSVNIGKGITLATTKDAYMGTGFRGRISCMQIYSSALTGPQISKLKNLCSKPGPFTPSIPVPRLPPAMAFYPLNVRYNTRDVSSNRNPPGRMGNVRPAFGPDLRPGGSFRFKGRSDSYIEFPNNGRLDTRKSLSIVAWINPAGPVGPIFNYKPDGFDVHMWMIRPRVLLVRFVNRLRRFTAPIETNLIKPKAWNFVTATYDQRSGDARIFIDSREVARKRIGQIRLATKYPAIMGARKGGKRFFQGRITCLQIYDIPLGPRQIREAKKLCLKTTCRANMDLAFLIDNSYYFRQRGQGAFSLLTRYIARILYSLRISRQGTRVSMATYASNARLLFPLSRYSRVSDILSALKRIRPRRGRLHLGRALYYVSSKIFPGRRRCGRKRVLVVFVSRRSQDSVERAARVLKRIGVEVFVVGIGGRVSRKELMKIATNGFHVFMASLRTLSTVLDTIRNKACSVTGSAAARAVFPLNGVTGGRDISINHNKAATLVNVKPAPGPDGLPLGSFLLRGIANSYIYFPNRGCMDTKNSMTIALWVYPESAGPIFHYFPKGRGVHLWMKDINTILVKFVPRSLQTISAVTSRRIKPTAWNFVAATYDYETGLASLWNDATLISQRNIGKIELATNYAAISGKKPRDKRIFRGRIACLQIFDRALTGRQLRAIKRKCFRARPSPTTPPPVLPLLVAVYPLDRINGVRDISPRRCPTGRRSNVGYAPGPDGRKDGATRFFGNAGSYIEIPNNGKLDTMVSTTILLWAYHEGLKGPLVNYRPGPGWGVNVWMMGPRTLLARFVRRDGVFTKAVMVTSRKIRYRAWNYFGATYDYKTGVAKLWVNSRLLVVQSIGRFRLATNYPIRLGARRNGKRFFKGRMFCLQIYSRALSRKEILAARSSCFRRFPTTTPTRKTKTPTTTPSPTRPKGPFRAAAFYPLNYLSRGRDRSLFRNPPGILGYVRSAPGPDKLPGGSYQFYGRPDSYIYLPNRGKLDTRKSISIIAWIRNDGGAGPIFHYMPNGWGVYLWMLSSNTVGVRFTRRQRRASTTMLSSRVITPHKWQYIAATYDYISGDARLYLDGNVIARKRLGRIRLATNYPVRIGAKKRDRRNFRGRISCVMVFDVALNSNQIARRKKRCFRRGPRGPSEKVCEPKIDLVFVVDACSENDRFTKANFRRVKNFLIGLIGDFVVSSKKVRISLVLFAQYPKLVLRFSTKKAFVFRIIRNMKLVCGARYSGAALKYAYRQILQRTTRKPVLVMMTTGGSRDDVRGPTALINRKRVETFAIGVGRRYSFRELQYIATDPRHVYTAAFRNLGSTVKLLKRKICKSDTLYHPA'
+    Bio::SignalP::Wrapper.new.calculate(big_seq, :binary_path => SIGNALP3_PATH).signal?.should == false
+  end
+end
+
+describe 'bio-signalp script' do
+  # Known to have a signal peptide
+  acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+
+  it "positive control" do
+    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
+
+    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
+    @result.should == [">positive\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n"]
+    @error.should == []
+  end
+
+  it "return gracefully when empty sequences are given" do
+    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
+
+    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
+    @result.should == [">positive\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n",
+    ">positive2\n", "FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ\n"]
+    @error.should == ["Unexpected empty sequence detected, ignoring: empty\n"]
+  end
+
+
+
+
+  it 'give the right -s output for signalp 3' do
+    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
+
+    # This also tests the -b flag
+    command = "#{command} -b #{SIGNALP3_PATH} -s"
+    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
+
+    expected = [
+    "Name\tNN Prediction\tHMM Prediction\n",
+    "positive\tT\tT\n"
+    ]
+    @result.should == expected
+    @error.should == []
+  end
+
+
+
+
+  it 'give the right -s output for signalp 4' do
+    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
+
+    command = "#{command} -b #{SIGNALP4_PATH} -s"
+    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
+
+    expected = [
+    "Name\tPredicted?\n",
+    "positive\tT\n"
+    ]
+    @result.should == expected
+    @error.should == []
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,13 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'rspec'
+require 'bio-signalp'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+
+end

metadata

@@ -1,110 +1,109 @@
 --- !ruby/object:Gem::Specification
 name: bio-signalp
 version: !ruby/object:Gem::Version
-  version: 0.3.0
-  prerelease: 
+  version: 0.3.1
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-18 00:00:00.000000000 Z
+date: 2014-08-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.1
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.1
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: bio-logger
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
 - !ruby/object:Gem::Dependency
-  name: shoulda
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '2.8'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '2.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.6.0
+        version: 1.0.21
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.6.0
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
 description: A wrapper for the signal peptide prediction algorith SignalP. Not very
@@ -117,7 +116,8 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
-- .document
+- ".document"
+- ".rspec"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -129,34 +129,30 @@ files:
 - lib/bio/appl/common.rb
 - lib/bio/appl/signalp3.rb
 - lib/bio/appl/signalp4.rb
-- test/helper.rb
-- test/test_bio-signalp.rb
+- spec/bio-signalp_spec.rb
+- spec/spec_helper.rb
 homepage: http://github.com/wwood/bioruby-signalp
 licenses:
 - MIT
+metadata: {}
 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: -969867473
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A wrapper for the signal peptide prediction algorith SignalP
 test_files: []

data/test/helper.rb

@@ -1,18 +0,0 @@
-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

@@ -1,159 +0,0 @@
-require 'helper'
-require 'open3'
-
-@@signalp3_path = File.join(ENV['HOME'],'bioinfo','signalp-3.0','signalp')
-@@signalp4_path = File.join(ENV['HOME'],'bioinfo','signalp-4.0','signalp')
-@@binaries = [
-  @@signalp3_path,
-  @@signalp4_path,
-]
-  
-class TestBioSignalp < Test::Unit::TestCase
-  def setup
-    log_name = 'bio-signalp'
-    Bio::Log::CLI.logger('stderr')
-    #Bio::Log::CLI.configure(log_name) # when commented out no debug is printed out
-  end
-
-  should "positive control" do
-  # 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
-    non_signal_sequence = 'KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK'
-
-    assert_equal false, Bio::SignalP::Wrapper.new.calculate(non_signal_sequence).signal?
-  end
-  
-  should 'work with different SignalP versions, this test is specific to Ben\'s machines probably' do
-    binaries = {
-      @@binaries[0] => Bio::SignalP::Version3::Result,
-      @@binaries[1] => Bio::SignalP::Version4::Result,
-    }
-    binaries.each do |binary, clazz|
-      acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
-      positive_result = Bio::SignalP::Wrapper.new.calculate(acp_sequence, :binary_path => binary)
-      assert_equal true, positive_result.signal?, binary
-      assert_kind_of clazz, positive_result, binary
-      assert_equal 17, positive_result.cleavage_site, binary
-      assert_equal 'FKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ',
-        positive_result.cleave(acp_sequence), binary
-      non_signal_sequence = 'KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK'
-      assert_equal false, Bio::SignalP::Wrapper.new.calculate(non_signal_sequence, :binary_path => binary).signal?, binary
-    end
-  end
-  
-  should 'give different predictions for v3 and v4' do
-    different = <<EOF
-MMKGMVEAAVKWMKAGLPLRILKLVLYAKVIDGDLQGHSLRRFSEVLKTFTELKERYEMQ
-LLLPKAVPLEFDVYLSFSEEDKEVAKVIREKLSGAKDGVRIYDSSHQGINKDTVFQEDMY
-SIMMKSARVVTVLSPNYLRNKACIEQYNIALCCNRRALRDMLAPIYVDSVEMMPTYMGLV
-QYVDCRPHDPSKIGEACSQLTVSLSVTFHTELRVAEFDPLRYDVFLSYSHRDTEKANRFV
-EMLQKLAPDLKLFFDVQELKTGKSWQRTLYHSIDGSRCMLALISEPYLKSAVCQEEFALA
-QAKHCAKGKQHLQLISICLDDLDTIQPEFTHIPMVKGTPDVFDDMVKTVCPAVIQWLNGE
-RVDQTETIKTLFDDQNITTLSADAEMEKFRQSHFQKEFGTQDSLISSKSPFPPKLSDILP
-EPGKEVKDKRPKSASDCDLIFSYHSDDEKYVSFIVKILQLNAPSLKVKAVCSDENKLSAF
-ERAHCIVPVLSPNYLESPECVEEFHIAIWRQRISNPEAGALLPICVHTLPQKPTYFHLVQ
-SAVSMTDGIWAQLSGQHNFGLPQKIVDFSLAAGKTPLSQVDMLALYMAAYYILKRFAKAR
-SCKEVEFSMKPALFNIMKLQEQIKQLTQPDYTDQLCKTLLEIHFNDIPDSWREGGHYLRP
-KEPEDTTPAIMAPVEGASDSQTHNALNERTQDSSGKDKSEVQGEKAQRSASEGVSHDTVQ
-QMDQDHDLKAAQGQDTAEGQDAAEGQDSEGGQDSEGGWDSDGGRDSVGNKTDAEKITGNH
-GDEGGDGQVGGSEESKEKTEDEDEDISKRNRAPRSVACVCL
-EOF
-    assert_equal true, Bio::SignalP::Wrapper.new.calculate(different, :binary_path => @@signalp3_path).signal?
-    assert_equal false, Bio::SignalP::Wrapper.new.calculate(different, :binary_path => @@signalp4_path).signal?
-  end
-end
-
-class TestSignalPScript < Test::Unit::TestCase
-  # Known to have a signal peptide
-  acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
-  
-  should "positive control" do
-    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
-    
-    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
-    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
-    
-    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
-  
-  
-  
-  
-  should 'give the right -s output for signalp 3' do
-    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
-    
-    # This also tests the -b flag
-    command = "#{command} -b #{@@signalp3_path} -s"
-    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
-    
-    expected = [
-    "Name\tNN Prediction\tHMM Prediction\n",
-    "positive\tT\tT\n"
-    ]
-    assert_equal expected, @result
-    assert_equal [], @error  
-  end
-  
-  
-  
-  
-  should 'give the right -s output for signalp 4' do
-    command = File.join(File.dirname(__FILE__),'..','bin','signalp.rb')
-    
-    command = "#{command} -b #{@@signalp4_path} -s"
-    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
-    
-    expected = [
-    "Name\tPredicted?\n",
-    "positive\tT\n"
-    ]
-    assert_equal [], @error
-    assert_equal expected, @result
-  end
-  
-end