bio 1.3.1 → 1.4.0

data/test/unit/bio/data/test_codontable.rb

@@ -4,14 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_codontable.rb,v 1.6 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__), ['..'] * 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/codontable'
 

data/test/unit/bio/data/test_na.rb

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005,2006 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_na.rb,v 1.9 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__), ['..'] * 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/na'
 

data/test/unit/bio/db/biosql/tc_biosql.rb

@@ -1,8 +1,12 @@
 # To change this template, choose Tools | Templates
 # and open the template in the editor.
 
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+# 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'
 

data/test/unit/bio/db/embl/test_common.rb

@@ -7,10 +7,12 @@
 #  $Id:$
 #
 
+# 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/db/embl/common'
 

data/test/unit/bio/db/embl/test_embl.rb

@@ -4,14 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_embl.rb,v 1.5.2.1 2008/02/20 09:56:22 aerts 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/db/embl/embl'
 
@@ -19,8 +20,7 @@ module Bio
   class TestEMBL < Test::Unit::TestCase
     
     def setup
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      output = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl')).read
+      output = File.read(File.join(BioRubyTestDataPath, 'embl', 'AB090716.embl'))
       @obj = Bio::EMBL.new(output)
     end
 

data/test/unit/bio/db/embl/test_embl_rel89.rb

@@ -4,14 +4,15 @@
 # Copyright::  Copyright (C) 2007 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_embl_rel89.rb,v 1.2.2.1 2008/02/20 09:56:22 aerts 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/db/embl/embl'
 
@@ -19,8 +20,7 @@ module Bio
   class TestEMBL89 < Test::Unit::TestCase
     
     def setup
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      output = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
+      output = File.read(File.join(BioRubyTestDataPath, 'embl', 'AB090716.embl.rel89'))
       @obj = Bio::EMBL.new(output)
     end
 

data/test/unit/bio/db/embl/test_embl_to_bioseq.rb

@@ -1,5 +1,5 @@
 #
-# test/unit/bio/db/embl/test_embl.rb - Unit test for Bio::EMBL
+# test/unit/bio/db/embl/test_embl_to_bioseq.rb - Unit test for Bio::EMBL to Bio::Sequence data converter
 #
 # Copyright::  Copyright (C) 2005, 2008
 #                 Mitsuteru Nakao <n@bioruby.org>
@@ -9,20 +9,20 @@
 #  $Id:$
 #
 
+# 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/db/embl/embl'
 
 module Bio
   class TestEMBLToBioSequence < Test::Unit::TestCase
     
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
+      input = File.read(File.join(BioRubyTestDataPath, 'embl', 'AB090716.embl.rel89'))
       embl_object = Bio::EMBL.new(input)
       embl_object.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
       @bio_seq = embl_object.to_biosequence
@@ -112,8 +112,7 @@ module Bio
   # that Bio::Sequence can be made into a valid Bio::EMBL again.
   class TestEMBLToBioSequenceRoundTrip < Test::Unit::TestCase
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
+      input = File.read(File.join(BioRubyTestDataPath, 'embl', 'AB090716.embl.rel89'))
       embl_object_1 = Bio::EMBL.new(input)
       embl_object_1.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
       @bio_seq_1 = embl_object_1.to_biosequence

data/test/unit/bio/db/embl/test_sptr.rb

@@ -7,11 +7,12 @@
 #  $Id:$
 #
 
+# 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/db/embl/sptr'
 
@@ -19,11 +20,8 @@ module Bio
   class TestSPTR < Test::Unit::TestCase
 
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), 
-                                            ['..'] * 5)).cleanpath.to_s
-      data = File.open(File.join(bioruby_root, 
-                                 'test', 'data', 'uniprot', 
-                                 'p53_human.uniprot')).read
+      data = File.read(File.join(BioRubyTestDataPath, 
+                                 'uniprot', 'p53_human.uniprot'))
       @obj = Bio::SPTR.new(data)
     end
 

data/test/unit/bio/db/embl/test_uniprot.rb

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_uniprot.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/db/embl/uniprot'
 
@@ -18,8 +20,7 @@ module Bio
   class TestUniProt < Test::Unit::TestCase
 
     def setup
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      data = File.open(File.join(bioruby_root, 'test', 'data', 'uniprot', 'p53_human.uniprot')).read
+      data = File.read(File.join(BioRubyTestDataPath, 'uniprot', 'p53_human.uniprot'))
       @obj = Bio::UniProt.new(data)
     end
 

data/test/unit/bio/db/fasta/test_format_qual.rb

@@ -0,0 +1,346 @@
+#
+# test/unit/bio/db/fasta/test_format_qual.rb - Unit test for Bio::Sequence::Format::Formatter::Fasta_numeric and Qual
+#
+# Copyright::  Copyright (C) 2009 Naohisa Goto
+# License::    The Ruby License
+#
+#  $Id:$
+#
+
+# 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/sequence'
+require 'bio/db/fasta/format_qual'
+
+module Bio
+  class TestSequenceFormatFormatterFasta_numeric < Test::Unit::TestCase
+
+    def setup
+      @sequence = Bio::Sequence.new('acgt' * 50 + 'a')
+      @sequence.quality_scores = (-100..100).to_a.freeze
+      @sequence.entry_id = 'TEST0001'
+      @sequence.definition = 'this is test'
+    end
+
+    def test_output
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -99 -98 -97 -96 -95 -94 -93 -92 -91 -90 -89 -88 -87 -86 -85 -84
+-83 -82 -81 -80 -79 -78 -77 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67
+-66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -55 -54 -53 -52 -51 -50
+-49 -48 -47 -46 -45 -44 -43 -42 -41 -40 -39 -38 -37 -36 -35 -34 -33
+-32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16
+-15 -14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9
+10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
+33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55
+56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
+79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
+_END_EXPECTED_
+
+      str = @sequence.output(:fasta_numeric)
+      assert_equal(expected, str)
+
+      # default width is 70
+      str = @sequence.output(:fasta_numeric, { :width => 70 })
+      assert_equal(expected, str)
+
+      # Modifying the sequence does not affect the output.
+      @sequence.delete!('a')
+      str = @sequence.output(:fasta_numeric)
+      assert_equal(expected, str)
+    end
+
+    def test_output_width_35
+      expected = <<_END_OF_EXPECTED_
+>TEST0001 this is test
+-100 -99 -98 -97 -96 -95 -94 -93
+-92 -91 -90 -89 -88 -87 -86 -85 -84
+-83 -82 -81 -80 -79 -78 -77 -76 -75
+-74 -73 -72 -71 -70 -69 -68 -67 -66
+-65 -64 -63 -62 -61 -60 -59 -58 -57
+-56 -55 -54 -53 -52 -51 -50 -49 -48
+-47 -46 -45 -44 -43 -42 -41 -40 -39
+-38 -37 -36 -35 -34 -33 -32 -31 -30
+-29 -28 -27 -26 -25 -24 -23 -22 -21
+-20 -19 -18 -17 -16 -15 -14 -13 -12
+-11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1
+0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26
+27 28 29 30 31 32 33 34 35 36 37 38
+39 40 41 42 43 44 45 46 47 48 49 50
+51 52 53 54 55 56 57 58 59 60 61 62
+63 64 65 66 67 68 69 70 71 72 73 74
+75 76 77 78 79 80 81 82 83 84 85 86
+87 88 89 90 91 92 93 94 95 96 97 98
+99 100
+_END_OF_EXPECTED_
+
+      str = @sequence.output(:fasta_numeric, { :width => 35 })
+      assert_equal(expected, str)
+    end
+
+    def test_output_width_nil
+      expected = ">TEST0001 this is test\n" + 
+        (-100..100).collect { |x| x.to_s }.join(' ') + "\n"
+      str = @sequence.output(:fasta_numeric, { :width => nil })
+      assert_equal(expected, str)
+    end
+
+  end #clsaa TestSequenceFormatFormatterFasta_numeric
+
+  class TestSequenceFormatFormatterQual < Test::Unit::TestCase
+    def setup
+      @sequence = Bio::Sequence.new('acgt' * 28)
+      @sequence.quality_scores = [ -100, *(-10..100).to_a ].freeze
+      @sequence.entry_id = 'TEST0001'
+      @sequence.definition = 'this is test'
+    end
+
+    def test_output
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
+38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
+84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
+_END_EXPECTED_
+
+      str = @sequence.output(:qual)
+      assert_equal(expected, str)
+
+      # default width is 70
+      str = @sequence.output(:qual, { :width => 70 })
+      assert_equal(expected, str)
+    end
+
+    def test_output_width45
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4
+5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
+22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
+37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
+52 53 54 55 56 57 58 59 60 61 62 63 64 65 66
+67 68 69 70 71 72 73 74 75 76 77 78 79 80 81
+82 83 84 85 86 87 88 89 90 91 92 93 94 95 96
+97 98 99 100
+_END_EXPECTED_
+
+      str = @sequence.output(:qual, { :width => 45 })
+      assert_equal(expected, str)
+    end
+
+    def test_output_after_truncating_sequence
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
+38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+61 62 63 64 65 66 67 68 69 70 71 72
+_END_EXPECTED_
+
+      # Modifying the sequence affects the output.
+      @sequence.delete!('a')
+      str = @sequence.output(:qual)
+      assert_equal(expected, str)
+    end
+
+    def test_output_after_adding_sequence
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
+38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
+84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+_END_EXPECTED_
+
+      # Modifying the sequence affects the output.
+      @sequence.gsub!(/a/, 'at')
+      str = @sequence.output(:qual)
+      assert_equal(expected, str)
+    end
+
+    def test_output_with_default_score
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
+38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
+84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 -10 -10 -10 -10
+-10 -10 -10 -10
+_END_EXPECTED_
+
+      # Modifying the sequence affects the output.
+      @sequence.concat('aaaatttt')
+      str = @sequence.output(:qual, { :default_score => -10 })
+      assert_equal(expected, str)
+    end
+
+    def test_output_with_converting_score_solexa2phred
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+0 0 1 1 1 1 1 1 2 2 3 3 4 4 5 5 6 7 8 9 10 10 11 12 13 14 15 16 17 18
+19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
+42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64
+65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87
+88 89 90 91 92 93 94 95 96 97 98 99 100 -99 -99 -99 -99
+_END_EXPECTED_
+
+      @sequence.quality_score_type = :solexa
+      @sequence.concat('aaaa')
+      str = @sequence.output(:qual, { :default_score => -99 })
+      assert_equal(expected, str)
+    end
+
+    def test_output_with_converting_score_phred2solexa
+      expected = <<_END_EXPECTED_
+>TEST0001 this is test
+-6 -2 0 2 3 5 6 7 8 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
+27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
+50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72
+73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95
+96 97 98 99 100 -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 -99
+_END_EXPECTED_
+
+      @sequence.quality_score_type = :phred
+      @sequence.quality_scores =
+        @sequence.quality_scores.find_all { |x| x > 0 }
+
+      str = @sequence.output(:qual,
+                             { :default_score => -99,
+                               :quality_score_type => :solexa
+                             })
+      assert_equal(expected, str)
+
+      # If @sequence.quality_score_type == nil, :phred is assumed.
+      @sequence.quality_score_type = nil
+      str = @sequence.output(:qual,
+                             { :default_score => -75,
+                               :quality_score_type => :solexa
+                             })
+      expected2 = expected.gsub(/ \-99/, ' -75')
+      assert_equal(expected2, str)
+    end
+
+    def test_output_from_error_probabilities
+      # @sequence.quality_scores
+      expected_qsc = <<_END_EXPECTED_
+>TEST0001 this is test
+-100 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
+38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
+84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
+_END_EXPECTED_
+
+      # @sequence.error_probabilities to phred score
+      expected_ep_phred = <<_END_EXPECTED_
+>TEST0001 this is test
+0 3 10 18 28 39 51 63 76 90 104 119 134 149 165 181 197 213 230 247
+264 282 300 317 336 354 372 391 409 428 447 467 486 505 525 545 565
+585 605 625 645 666 686 707 727 748 769 790 811 832 854 875 897 918
+940 962 983 1005 1027 1049 1071 1093 1116 1138 1160 1183 1205 1228
+1250 1273 1296 1319 1342 1365 1388 1411 1434 1457 1480 1503 1527 1550
+1574 1597 1621 1644 1668 1692 1715 1739 1763 1787 1811 1835 1859 1883
+1907 1931 1956 1980 2004 2029 2053 2078 2102 2127 2151 2176 2200 2225
+2250 2275
+_END_EXPECTED_
+
+      # @sequence.error_probabilities to phred score
+      expected_ep_solexa = <<_END_EXPECTED_
+>TEST0001 this is test
+-80 0 9 18 28 39 51 63 76 90 104 119 134 149 165 181 197 213 230 247
+264 282 300 317 336 354 372 391 409 428 447 467 486 505 525 545 565
+585 605 625 645 666 686 707 727 748 769 790 811 832 854 875 897 918
+940 962 983 1005 1027 1049 1071 1093 1116 1138 1160 1183 1205 1228
+1250 1273 1296 1319 1342 1365 1388 1411 1434 1457 1480 1503 1527 1550
+1574 1597 1621 1644 1668 1692 1715 1739 1763 1787 1811 1835 1859 1883
+1907 1931 1956 1980 2004 2029 2053 2078 2102 2127 2151 2176 2200 2225
+2250 2275
+_END_EXPECTED_
+
+      @sequence.error_probabilities =
+        (0...(@sequence.length)).collect { |i| ((i + 1) ** -i) }
+      # Because Solexa score does not allow 1.
+      @sequence.error_probabilities[0] = 0.99999999
+
+      # @sequence.quality_score_type: nil
+      # output :qual, :quality_score_type => (not set)
+      #
+      # ==> using @sequence.quality_scores
+      #
+      @sequence.quality_score_type = nil
+      str = @sequence.output(:qual)
+      assert_equal(expected_qsc, str)
+
+      # @sequence.quality_score_type: :phred
+      # output :qual, :quality_score_type => (not set)
+      #
+      # ==> using @sequence.error_probabilities
+      #
+      @sequence.quality_score_type = :phred
+      str = @sequence.output(:qual)
+      assert_equal(expected_ep_phred, str)
+
+      # @sequence.quality_score_type: nil
+      # output :qual, :quality_score_type => :phred
+      #
+      # ==> using @sequence.error_probabilities
+      #
+      @sequence.quality_score_type = nil
+      str = @sequence.output(:qual, :quality_score_type => :phred)
+      assert_equal(expected_ep_phred, str)
+
+      # @sequence.quality_score_type: :phred
+      # output :qual, :quality_score_type => :solexa
+      #
+      # ==> using @sequence.error_probabilities
+      #
+      @sequence.quality_score_type = :phred
+      str = @sequence.output(:qual, :quality_score_type => :solexa)
+      assert_equal(expected_ep_solexa, str)
+
+      # @sequence.quality_score_type: :solexa
+      # output :qual, :quality_score_type => :phred
+      #
+      # ==> using @sequence.error_probabilities
+      #
+      @sequence.quality_score_type = :solexa
+      str = @sequence.output(:qual, :quality_score_type => :phred)
+      assert_equal(expected_ep_phred, str)
+
+      # @sequence.quality_score_type: :phred
+      # output :qual, :quality_score_type => :phred
+      #
+      # ==> using @sequence.quality_scores
+      #
+      @sequence.quality_score_type = :phred
+      str = @sequence.output(:qual, :quality_score_type => :phred)
+      assert_equal(expected_qsc, str)
+
+      # After removing @sequence.quality_scores:
+      # @sequence.quality_score_type: :phred
+      # output :qual, :quality_score_type => :phred
+      #
+      # ==> using @sequence.error_probabilities
+      #
+      @sequence.quality_scores = nil
+      @sequence.quality_score_type = :phred
+      str = @sequence.output(:qual, :quality_score_type => :phred)
+      assert_equal(expected_ep_phred, str)
+    end
+
+  end #class TestSequenceFormatFormatterQual
+
+end #module Bio
+
+