executable: use ARGF instead of ARGV[0]

Gemfile

@@ -10,6 +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

Rakefile

@@ -32,22 +32,14 @@ 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'
 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

bin/signalp.rb

@@ -71,7 +71,7 @@
     ].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']
       puts [

test/test_bio-signalp.rb

@@ -1,17 +1,39 @@
 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
+  should "positive control" do
+  # Known to have a signal peptide
+    acp_sequence = 'MKILLLCIIFLYYVNAFKNTQKDGVSLQILKKKRSNQVNFLNRKNDYNLIKNKNPSSSLKSTFDDIKKIISKQLSVEEDKIQMNSNFTKDLGADSLDLVELIMALEEKFNVTISDQDALKINTVQDAIDYIEKNNKQ'
+
+    command = "RUBYLIB="+
+    File.join(File.dirname(__FILE__),'..','lib')+' '+
+    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
+    p @result
+    p @error
+  end
+end