bio 1.3.1 → 1.4.0

data/test/unit/bio/appl/mafft/test_report.rb

@@ -5,16 +5,17 @@
 #              2005 Naohisa Goto <ng@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_report.rb,v 1.1 2007/07/16 12:21:39 ngoto Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
-
-require 'bio'
+require 'bio/appl/mafft/report'
 
 module Bio
   class TestAlignmentMultiFastaFormat < Test::Unit::TestCase

data/test/unit/bio/appl/meme/mast/test_report.rb

@@ -0,0 +1,46 @@
+#
+# test/unit/bio/appl/meme/test_mast.rb - Unit test for Bio::Meme::Mast::Report
+#
+# Copyright::  Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/appl/meme/mast/report'
+
+module Bio
+module TestMastReportData
+  
+  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'meme')).cleanpath.to_s
+  
+  def self.example_mast_output
+    File.join TEST_DATA, 'mast.out'
+  end
+  
+end
+class TestMastReport < Test::Unit::TestCase
+  
+  TEST_DATA = TestMastReportData::TEST_DATA
+  
+  def setup
+    @report = Meme::Mast::Report.new(File.read(TestMastReportData.example_mast_output))
+  end
+  
+  def test_report_has_motifs
+    obj = @report.motifs.first
+    assert_kind_of(Meme::Motif, obj)
+  end
+  
+  def test_parse_hit_list_with_bad_data
+    data = "#heres\n2 bad data lines\n"
+    assert_raises(RuntimeError) { Meme::Mast::Report.new(data) }
+  end
+  
+end # TestMastReport
+end # Bio

data/test/unit/bio/appl/meme/test_mast.rb

@@ -0,0 +1,103 @@
+#
+# test/unit/bio/appl/meme/test_mast.rb - Unit test for Bio::Meme::Mast
+#
+# Copyright::  Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/appl/meme/mast'
+
+module Bio
+module TestMastData
+  
+  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'meme')).cleanpath.to_s
+  
+  def self.example_mfile
+    File.join TEST_DATA, 'meme.out'
+  end
+  
+  def self.dummy_binary
+    File.join TEST_DATA, 'mast'
+  end
+  
+  def self.dummy_db
+    File.join TEST_DATA, 'db'
+  end
+end
+
+class TestMast < Test::Unit::TestCase
+  
+  TEST_DATA = TestMastData::TEST_DATA
+  
+  def setup
+    @example_mfile = TestMastData.example_mfile
+    @binary = TestMastData.dummy_binary
+    @db = TestMastData.dummy_db
+    @mast = Meme::Mast.new(@binary)
+  end
+  
+  def test_config_defaults
+    assert_equal(true, @mast.options[:hit_list])
+    assert_equal(true, @mast.options[:stdout])
+    assert_equal(true, @mast.options[:nostatus])
+  end
+  
+  def test_minimal_config
+    options = {:mfile => @example_mfile, :d => @db}
+    @mast.config(options)
+    assert_equal(@db, @mast.options[:d])
+    assert_equal(@example_mfile, @mast.options[:mfile])
+  end
+  
+  def test_more_config
+    options = {:mfile => @example_mfile, :d => @db, :dna => true}
+    @mast.config(options)
+    assert_equal(true, @mast.options[:dna])
+  end
+  
+  def test_check_options_with_valid_opts
+    options = {:mfile => @example_mfile, :d => @db}
+    @mast.config(options)
+    assert_nothing_raised { @mast.check_options }
+  end
+  
+  def test_check_options_with_invalid_opts
+    options = {:mfile => @example_mfile, :d => @db, :bad => "option"}
+    @mast.config(options)
+    assert_raises(ArgumentError) { @mast.check_options }
+  end
+  
+  def test_check_options_with_empty_opts
+    # <mfile> and <-d> are required
+    options = {}
+    @mast.config(options)
+    assert_raises(ArgumentError) { @mast.check_options }
+  end
+  
+  # this is ugly
+  def test_command_to_be_run
+    options = {:mfile => @example_mfile, :d => @db}
+    @mast.config(options)
+    assert_equal(true, @mast.cmd.include?("#{@binary} #{@example_mfile} -d #{@db}") )
+    assert_equal(true, @mast.cmd.include?('-hit_list') )
+    assert_equal(true, @mast.cmd.include?('-stdout') )
+    assert_equal(true, @mast.cmd.include?('-nostatus') )
+  end
+  
+  # this would require a working executable and a database
+  def test_run
+    # options = {:mfile => @example_mfile, :d => @db}
+    # @mast.config(options)
+    # report = @mast.run
+    # assert_kind_of(Meme::Mast::Report, report)
+  end
+  
+end # TestMast
+end # Bio

data/test/unit/bio/appl/meme/test_motif.rb

@@ -0,0 +1,38 @@
+#
+# test/unit/bio/appl/meme/test_motif.rb - Unit test for Bio::Meme::Motif
+#
+# Copyright::  Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>
+# License::    The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/appl/meme/motif'
+
+module Bio
+  class TestMotif < Test::Unit::TestCase
+    
+    def setup
+      @motif = Meme::Motif.new("P12345", "A", "1", "10", "30", "1.0e-100")
+    end
+    
+    def test_creation_and_attributes
+      assert_equal("P12345", @motif.sequence_name)
+      assert_equal("A", @motif.strand)
+      assert_equal(1, @motif.motif)
+      assert_equal(10, @motif.start_pos)
+      assert_equal(30, @motif.end_pos)
+      assert_equal(1.0e-100, @motif.pvalue)
+    end
+    
+    def test_length
+      assert_equal(20, @motif.length)
+    end
+    
+  end # TestMotif
+end # Bio

data/test/unit/bio/appl/paml/codeml/test_rates.rb

@@ -5,18 +5,19 @@
 # License::    The Ruby License
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/paml/codeml/rates'
 
 module Bio; module TestPAMLCodeml
 class TestCodemlRates < Test::Unit::TestCase
 
-  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
-  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
 
   def setup
     str = File.read(File.join(TEST_DATA, 'rates'))

data/test/unit/bio/appl/paml/codeml/test_report.rb

@@ -5,18 +5,19 @@
 # License::    The Ruby License
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/paml/codeml/report'
 
 module Bio; module TestPAMLCodeml
 class TestCodemlReport < Test::Unit::TestCase
 
-  bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6)).cleanpath.to_s
-  TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+  TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
 
   def setup
     str = File.read(File.join(TEST_DATA, 'output.txt'))

data/test/unit/bio/appl/paml/test_codeml.rb

@@ -5,18 +5,19 @@
 # License::    The Ruby License
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/paml/codeml'
 
 module Bio; module TestPAMLCodeml
   module TestCodemlData
 
-    bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-    TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'paml', 'codeml')).cleanpath.to_s
+    TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'paml', 'codeml')).cleanpath.to_s
 
     def self.example_control
       File.join TEST_DATA, 'control_file.txt'

data/test/unit/bio/appl/sim4/test_report.rb

@@ -8,18 +8,19 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/sim4/report'
 
 module Bio
 
   class TestDataForSim4Report
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-    DataPath = Pathname.new(File.join(bioruby_root, 'test', 'data', 'sim4')).cleanpath.to_s
+    DataPath = Pathname.new(File.join(BioRubyTestDataPath, 'sim4')).cleanpath.to_s
 
     def initialize(filename)
       @filename = filename

data/test/unit/bio/appl/sosui/test_report.rb

@@ -4,21 +4,22 @@
 # Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/sosui/report'
 
 
 module Bio
 
-  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-  test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'SOSUI')).cleanpath.to_s
+  test_data = Pathname.new(File.join(BioRubyTestDataPath, 'SOSUI')).cleanpath.to_s
   SOSUIReport = File.open(File.join(test_data, 'sample.report')).read
 
 

data/test/unit/bio/appl/targetp/test_report.rb

@@ -4,13 +4,15 @@
 # Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::   The Ruby License
 #
-#  $Id: test_report.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/targetp/report'
 

data/test/unit/bio/appl/test_blast.rb

@@ -7,18 +7,19 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/blast'
 
 
 module Bio
   class TestBlastData
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
-    TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
+    TestDataBlast = Pathname.new(File.join(BioRubyTestDataPath, 'blast')).cleanpath.to_s
 
     def self.input
       File.open(File.join(TestDataBlast, 'b0002.faa')).read

data/test/unit/bio/appl/test_fasta.rb

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/fasta'
 

data/test/unit/bio/appl/test_pts1.rb

@@ -8,10 +8,12 @@
 # $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/pts1'
 

data/test/unit/bio/appl/tmhmm/test_report.rb

@@ -4,21 +4,22 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_report.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/tmhmm/report'
 
 
 module Bio
 
-  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-  test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'TMHMM')).cleanpath.to_s
+  test_data = Pathname.new(File.join(BioRubyTestDataPath, 'TMHMM')).cleanpath.to_s
   TMHMMReport = File.open(File.join(test_data, 'sample.report')).read
 
 

data/test/unit/bio/data/test_aa.rb

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_aa.rb,v 1.7 2007/04/06 04:46:36 k Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/data/aa'