bioinform 0.1.17 → 0.2.0

data/spec/data_models/ppm_spec.rb

@@ -1,54 +1,57 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/data_models/pcm'
-
-module Bioinform
-  describe PPM do
-    describe '#to_ppm' do
-      let (:ppm_motif) { Fabricate(:ppm) }
-      it 'returns self' do
-         ppm_motif.to_ppm.should eq ppm_motif
-      end
-    end
+require 'bioinform/data_models/ppm'
 
-    describe '#to_pcm' do
-      let (:ppm_motif) { Fabricate(:ppm_by_pcm) }
-      let (:pcm_motif) { Fabricate(:pcm) }
+describe Bioinform::MotifModel::PPM do
 
-      it 'returns pcm using given effective_count' do
-        ppm = ppm_motif.tap{|ppm| ppm.effective_count = pcm_motif.count }
-        ppm.to_pcm.should == pcm_motif
-      end
-      it 'without given count it raises an error' do
-        expect{ ppm_motif.to_pcm }.to raise_error
+  describe '.new' do
+    specify 'fails on matrix having negative elements' do
+      expect { Bioinform::MotifModel::PPM.new([[0.4, 0.1, 0.1, 0.4],[0.6, -0.1, -0.1, 0.6],[0.25, 0.25, 0.25, 0.25]]) }.to raise_error (Bioinform::Error)
+    end
+    specify 'fails on matrix having sum of position elements different from 1' do
+      expect { Bioinform::MotifModel::PPM.new([[0.4, 0.1, 0.1, 0.4],[0.6, 0.1, 0.1, 0.6],[0.25, 0.25, 0.25, 0.25]]) }.to raise_error (Bioinform::Error)
+      expect { Bioinform::MotifModel::PPM.new([[0.4, 0.1, 0.1, 0.4],[0.3, 0.1, 0.1, 0.3],[0.25, 0.25, 0.25, 0.25]]) }.to raise_error (Bioinform::Error)
+      expect { Bioinform::MotifModel::PPM.new([[0.3, 0.1, 0.1, 0.3],[0.3, 0.1, 0.1, 0.3],[0.2, 0.2, 0.2, 0.2]]) }.to raise_error (Bioinform::Error)
+    end
+
+    context 'with valid matrix' do
+      let(:matrix) { [[0.4, 0.1, 0.1, 0.4],[0.3, 0.2, 0.2, 0.3],[0.25, 0.25, 0.25, 0.25]] }
+      specify do
+        expect { Bioinform::MotifModel::PPM.new(matrix) }.not_to raise_error
       end
-      it 'returns pcm with the same name' do
-        ppm = ppm_motif.tap{|ppm| ppm.effective_count = pcm_motif.count }
-        ppm.to_pcm.name.should == ppm_motif.name
+      specify do
+        expect( Bioinform::MotifModel::PPM.new(matrix).matrix ).to eq matrix
       end
     end
+  end
+
+  describe '.from_string' do
+    specify {
+      expect( Bioinform::MotifModel::PPM.from_string("0.1 0.2 0.3 0.4\n0.4 0.2 0.2 0.2").model.class ).to eq Bioinform::MotifModel::PPM
+    }
+  end
 
-    describe '#to_pwm' do
-      let (:ppm_motif_without_count) { Fabricate(:ppm_by_pcm) }
-      let (:ppm_motif) { ppm_motif_without_count.tap{|ppm| ppm.effective_count = 137 } }
-      let (:ppm_motif_with_log_pseudocount) { ppm_motif.tap{|ppm| ppm.effective_count = 137 } }
-      let (:pcm_motif) { ppm_motif.to_pcm }
+  context 'valid PPM' do
+    let(:ppm) { Bioinform::MotifModel::PPM.new(matrix) }
+    let(:matrix) { [[0.4, 0.1, 0.1, 0.4],[0.3, 0.2, 0.2, 0.3],[0.25, 0.25, 0.25, 0.25]] }
 
-      it 'returns pwm the same as pwm of according pcm' do
-        ppm_motif.to_pwm.should == pcm_motif.to_pwm
-      end
-      it 'uses pseudocount to transform according pcm to pwm' do
-        ppm = ppm_motif.tap{|ppm| ppm.pseudocount = 10}
-        ppm_motif.to_pwm.should == pcm_motif.to_pwm(10)
-      end
-      it 'by default uses pseudocount equal to log of count' do
-        ppm_motif.to_pwm.should == ppm_motif.to_pcm.to_pwm(Math.log(137))
-      end
-      it 'without given count it raises an error' do
-        expect{ ppm_motif_without_count.to_pwm }.to raise_error
-      end
-      it 'returns pwm with the same name' do
-        ppm_motif.to_pwm.name.should == ppm_motif.name
-      end
+    specify { expect(ppm).to eq Bioinform::MotifModel::PPM.new(matrix) }
+    specify { expect(ppm).not_to eq matrix }
+    specify { expect(ppm).not_to eq Bioinform::MotifModel::PM.new(matrix) }
+    specify { expect(ppm).not_to eq Bioinform::MotifModel::PWM.new(matrix) }
+    specify { expect(ppm).not_to eq Bioinform::MotifModel::PCM.new(matrix) }
+    specify { expect(matrix).not_to eq ppm }
+    specify { expect(Bioinform::MotifModel::PM.new(matrix)).not_to eq ppm }
+    specify { expect(Bioinform::MotifModel::PWM.new(matrix)).not_to eq ppm }
+    specify { expect(Bioinform::MotifModel::PCM.new(matrix)).not_to eq ppm }
+
+    specify { expect(ppm.named('motif name')).to be_kind_of Bioinform::MotifModel::NamedModel }
+    specify { expect(ppm.named('motif name').model).to eq ppm }
+    specify { expect(ppm.named('motif name').name).to eq 'motif name' }
+
+    describe '#reversed, #complemented, #reverse_complemented' do
+      specify { expect(ppm.reversed).to be_kind_of Bioinform::MotifModel::PPM }
+      specify { expect(ppm.complemented).to be_kind_of Bioinform::MotifModel::PPM }
+      specify { expect(ppm.reverse_complemented).to be_kind_of  Bioinform::MotifModel::PPM }
+      specify { expect(ppm.revcomp).to be_kind_of             Bioinform::MotifModel::PPM }
     end
   end
 end

data/spec/data_models/pwm_spec.rb

@@ -1,96 +1,104 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/data_models/pwm'
+require 'bioinform/data_models/pwm'
 
-module Bioinform
-  describe PWM do
-    describe '#score_mean' do
-      it 'should be equal to a mean score of pwm' do
-        pwm = PWM.new( [[1,2,1,2],[4,6,8,6],[2,2,2,2]] )
-        pwm.score_mean.should == 1.5 + 6 + 2
+describe Bioinform::MotifModel::PWM do
+
+  describe '.new' do
+    context 'with valid matrix' do
+      let(:matrix) { [[1,2,3,1.567],[12,-11,12,0],[-1.1, 0.6, 0.4, 0.321]] }
+
+      specify do
+        expect { Bioinform::MotifModel::PWM.new(matrix) }.not_to raise_error
       end
-      it 'should be equal to a mean score of pwm by measure induced from background probability mean' do
-        pwm = PWM.new( [[1,2,1,2],[4,6,8,6],[2,2,2,2]] ).set_parameters(background: [0.2, 0.3, 0.3, 0.2])
-        pwm.score_mean.should == ((0.2*1+0.3*2+0.3*1+0.2*2) + (0.2*4+0.3*6+0.3*8+0.2*6) + (0.2*2+0.3*2+0.3*2+0.2*2)) / (0.2+0.3+0.3+0.2)
+      specify do
+        expect( Bioinform::MotifModel::PWM.new(matrix).matrix ).to eq matrix
       end
     end
+  end
 
-    describe '#score_variance' do
-    end
+  context 'valid PWM' do
+    let(:matrix) { [[1,2,3,1.567],[12,-11,12,0],[-1.1, 0.6, 0.4, 0.321]] }
+    let(:pwm) { Bioinform::MotifModel::PWM.new(matrix) }
 
-    describe '#gauss_estimation' do
-    end
+    specify { expect(pwm).to eq Bioinform::MotifModel::PWM.new(matrix) }
+    specify { expect(pwm).not_to eq matrix }
+    specify { expect(pwm).not_to eq Bioinform::MotifModel::PM.new(matrix) }
+    # specify { expect(pwm).not_to eq Bioinform::MotifModel::PCM.new(matrix) }
+    # specify { expect(pwm).not_to eq Bioinform::MotifModel::PPM.new(matrix) }
+    specify { expect(matrix).not_to eq pwm }
+    specify { expect(Bioinform::MotifModel::PM.new(matrix)).not_to eq pwm }
+    # specify { expect(Bioinform::MotifModel::PCM.new(matrix)).not_to eq pwm }
+    # specify { expect(Bioinform::MotifModel::PPM.new(matrix)).not_to eq pwm }
+
+    specify { expect(pwm.named('motif name')).to be_kind_of Bioinform::MotifModel::NamedModel }
+    specify { expect(pwm.named('motif name').model).to eq pwm }
+    specify { expect(pwm.named('motif name').name).to eq 'motif name' }
 
     describe '#score' do
-      let(:pwm) do
-        PWM.new( [[10000,20000,30000,40000],[1000,2000,3000,4000],[100,200,300,400],[10,20,30,40],[1,2,3,4]] )
-      end
-      it 'should evaluate to score of given word' do
-        pwm.score('aAAAA').should == 11111
-        pwm.score('agata').should == 13141
-        pwm.score('CCGCT').should == 22324
-      end
-      it 'should give score average score(considering probabilities) for a position for a N-letter' do
-        pwm.score('AANAA').should == (11011 + 250)
-        pwm.set_parameters(background: [0.1,0.4,0.1,0.4]).score('AANAA').should == (11011 + 0.1*100 + 0.4*200 + 0.1*300 + 0.4*400)
-      end
-      it 'should raise an ArgumentError if word contain bad letter' do
-        expect{ pwm.score('AAAAV') }.to raise_error(ArgumentError)
-      end
-      it 'should raise an ArgumentError if word has size different than size of matrix' do
-        expect{ pwm.score('AAA') }.to raise_error(ArgumentError)
-      end
+      specify { expect( pwm.score('acT') ).to eq(1 + (-11) + 0.321) }
+      specify { expect{ pwm.score('acTt') }.to raise_error(Bioinform::Error) }
+      specify { expect{ pwm.score('ac') }.to raise_error(Bioinform::Error) }
+      specify { expect{ pwm.score('acW') }.to raise_error(Bioinform::Error) }
+      specify { expect{ pwm.score('acN') }.to raise_error(Bioinform::Error) }
     end
 
-    describe '#best_score' do
-      it 'should be equal to best score' do
-        @pwm = PWM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
-        @pwm.best_score.should == 4.9 + 7.13 + (-1.0)
-      end
+    describe '#reversed, #complemented, #reverse_complemented' do
+      specify { expect(pwm.reversed).to be_kind_of Bioinform::MotifModel::PWM }
+      specify { expect(pwm.complemented).to be_kind_of Bioinform::MotifModel::PWM }
+      specify { expect(pwm.reverse_complemented).to be_kind_of  Bioinform::MotifModel::PWM }
+      specify { expect(pwm.revcomp).to be_kind_of             Bioinform::MotifModel::PWM }
     end
-    describe '#worst_score' do
-      it 'should be equal to worst score' do
-        @pwm = PWM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
-        @pwm.worst_score.should == 1.3 + 3.25 + (-1.5)
-      end
+
+    describe '#discreted' do
+      specify { expect(pwm.discreted(1)).to eq Bioinform::MotifModel::PWM.new( [[1,2,3,2],[12,-11,12,0],[-1, 1, 1, 1]]) }
+      specify { expect(pwm.discreted(1, rounding_method: :round)).to eq Bioinform::MotifModel::PWM.new( [[1,2,3,2],[12,-11,12,0],[-1, 1, 0, 0]]) }
+      specify { expect(pwm.discreted(10)).to eq Bioinform::MotifModel::PWM.new( [[10,20,30,16],[120,-110,120,0],[-11, 6, 4, 4]]) }
+      specify { expect(pwm.discreted(10, rounding_method: :round)).to eq Bioinform::MotifModel::PWM.new( [[10,20,30,16],[120,-110,120,0],[-11, 6, 4, 3]]) }
+      specify { expect(pwm.discreted(10, rounding_method: :floor)).to eq Bioinform::MotifModel::PWM.new( [[10,20,30,15],[120,-110,120,0],[-11, 6, 4, 3]]) }
     end
 
-    describe '#best_suffix' do
-      it 'should return maximal score of suffices from i-th position inclusively i.e. [i..end]' do
-        @pwm = PWM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
-        @pwm.best_suffix(0).should == (4.9 + 7.13 - 1.0)
-        @pwm.best_suffix(1).should == (7.13 - 1.0)
-        @pwm.best_suffix(2).should == (-1.0)
-        @pwm.best_suffix(3).should == (0.0)
-      end
-      it 'should give right results after left(right)_augment, discrete, reverse_complement etc' do
-        pwm = PWM.new([[1, 2, 3, 4], [10,10.5,11,11.5]])
-        pwm.best_suffix(1).should == 11.5
-        pwm.left_augment!(1)
-        pwm.best_suffix(1).should == 15.5
-      end
+    describe '#left_augmented' do
+      specify { expect{pwm.left_augmented(-1)}.to raise_error Bioinform::Error }
+      specify { expect(pwm.left_augmented(0)).to eq pwm }
+      specify { expect(pwm.left_augmented(2)).to eq Bioinform::MotifModel::PWM.new( [[0,0,0,0],[0,0,0,0],[1,2,3,1.567],[12,-11,12,0],[-1.1, 0.6, 0.4, 0.321]]) }
     end
-    describe '#worst_suffix' do
-      it 'should return minimal score of suffices from i-th position inclusively i.e. [i..end]' do
-        @pwm = PWM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
-        @pwm.worst_suffix(0).should == (1.3 + 3.25 - 1.5)
-        @pwm.worst_suffix(1).should == (3.25 - 1.5)
-        @pwm.worst_suffix(2).should == (- 1.5)
-        @pwm.worst_suffix(3).should == (0.0)
-      end
+    describe '#right_augmented' do
+      specify { expect{pwm.right_augmented(-1)}.to raise_error Bioinform::Error }
+      specify { expect(pwm.right_augmented(0)).to eq pwm }
+      specify { expect(pwm.right_augmented(2)).to eq Bioinform::MotifModel::PWM.new( [[1,2,3,1.567],[12,-11,12,0],[-1.1, 0.6, 0.4, 0.321],[0,0,0,0],[0,0,0,0]]) }
     end
+  end
 
-    describe '#round' do
-      let(:matrix) { [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -0.5, -1.5, -1.0]] }
-      let(:pm) { PWM.new( matrix ).tap{|pm| pm.name = 'motif name'} }
-      it 'gives model with matrix elements rounded' do
-        pm.round(1).matrix.should == [[1.3, 2.0, 4.9, 3.2], [7.1, 6.5, 3.3, 4.6], [-1.0, -0.5, -1.5, -1.0]]
-      end
-      it 'gives PWM model' do
-        pm.round(1).should be_kind_of(PWM)
-      end
-      it 'gives model with the same name' do
-        pm.round(1).name.should == 'motif name'
-      end
+  context 'with different alphabet' do
+                  #  A     C    G    T       M  R  W  S  Y  K   B   D   H   V     N
+    let(:matrix) { [[1,    2,   3,   1.567,  10,20,30,40,50,60, 700,800,900,1000, 10000],
+                    [12,  -11,  12,  0,      11,21,31,41,51,61, 701,801,901,1001, 10001 ],
+                    [-1.1, 0.6, 0.4, 0.321,  12,22,32,42,52,62, 702,802,902,1002, 10002 ]] }
+    let(:pwm) { Bioinform::MotifModel::PWM.new(matrix, alphabet: Bioinform::IUPACAlphabet) }
+    describe '#score' do
+      specify { expect( pwm.score('acT') ).to eq(1 + (-11) + 0.321) }
+      specify { expect{ pwm.score('acTt') }.to raise_error(Bioinform::Error) }
+      specify { expect{ pwm.score('ac') }.to raise_error(Bioinform::Error) }
+      specify { expect( pwm.score('acW') ).to eq(1 + (-11) + 32) }
+      specify { expect( pwm.score('acN') ).to eq(1 + (-11) + 10002) }
     end
+    specify { expect(pwm.left_augmented(1)).to be_kind_of Bioinform::MotifModel::PWM }
+    specify { expect(pwm.left_augmented(1).alphabet).to eq Bioinform::IUPACAlphabet }
+    specify { expect(pwm.left_augmented(1).matrix).to eq [[0,    0,   0,   0,      0, 0, 0, 0, 0, 0,  0,  0,  0,  0,    0],
+                                                        [1,    2,   3,   1.567,  10,20,30,40,50,60, 700,800,900,1000, 10000],
+                                                        [12,  -11,  12,  0,      11,21,31,41,51,61, 701,801,901,1001, 10001 ],
+                                                        [-1.1, 0.6, 0.4, 0.321,  12,22,32,42,52,62, 702,802,902,1002, 10002 ]] }
+
+    specify { expect(pwm.discreted(1).matrix).to eq [[1, 2, 3, 2,  10,20,30,40,50,60, 700,800,900,1000, 10000],
+                                                    [12,-11,12,0,  11,21,31,41,51,61, 701,801,901,1001, 10001 ],
+                                                    [-1, 1, 1, 1,  12,22,32,42,52,62, 702,802,902,1002, 10002 ]] }
+    specify { expect(pwm.discreted(1).alphabet).to eq Bioinform::IUPACAlphabet}
+
+    specify { expect{ pwm.to_IUPAC_PWM }.to raise_error }
+  end
+
+  describe '.from_string' do
+    specify {
+      expect( Bioinform::MotifModel::PWM.from_string("1 2 3 4\n5 6 7 8").model.class ).to eq Bioinform::MotifModel::PWM
+    }
   end
 end

data/spec/fabricators/motif_formats_fabricator.rb

@@ -1,125 +1,125 @@
-require_relative '../../lib/bioinform/support/strip_doc'
-require 'ostruct'
+# require_relative '../../lib/bioinform/support/strip_doc'
+# require 'ostruct'
 
-Fabricator(:SP1_f1_plain_text, class_name: OpenStruct) do
-  name 'SP1_f1'
-  pcm (<<-EOS).strip_doc
-    SP1_f1
-    682.6436366358055  443.1455214015781  2075.655346294993  287.211468117951
-    299.8883246804867  103.74338315843572  2613.8927022405364  471.1315623708902
-    591.4892493324709  42.631827541794564  2845.1654083148564  9.36948726124641
-    7.071084742361592  45.29093411231232  3432.8847704374107  3.409183158303573
-    91.308984085713  19.1536481364332  3373.656949880137  4.5363903481026
-    809.2082973387932  2246.941954176211  61.30766021687515  371.19806071846244
-    120.56476435866055  42.4349244403591  3242.1560628684038  83.50022078295852
-    13.72524477409959  35.858220519297525  3332.4066864946167  106.66582066236779
-    558.1188080161639  90.0084504200356  2694.854973210736  145.67374080342415
-    264.0088462230318  254.7175868081866  2796.88087480315  173.0486646159857
-    519.46013914282  1874.9349086474765  654.5411208373813  439.7198038226514
-  EOS
-  pwm (<<-EOS).strip_doc
-    SP1_f1
-    -0.24435707885585292	-0.674823404693731	0.8657012535789866	-1.1060188862599287
-    -1.0631255752097797	-2.111925969423868	1.0960627561110403	-0.6138563775211977
-    -0.3872276234760535	-2.9739851913218045	1.1807800242010378	-4.338927525031566
-    -4.563896055436894	-2.9161633002532277	1.3684371349982638	-5.077972423609655
-    -2.2369752892820083	-3.7196436313301846	1.3510439136452734	-4.889930670508233
-    -0.07473964149330865	0.944919654762011	-2.6246857648086044	-0.8510983487822436
-    -1.9643526491643322	-2.978402770880115	1.3113096718240573	-2.324334259499025
-    -4.0155484139655835	-3.1384268078096667	1.3387488589788057	-2.084673903537648
-    -0.44509385828355363	-2.2510053061629702	1.1265431574368685	-1.7780413702431372
-    -1.1896356092245048	-1.2251832285630027	1.1636760063747527	-1.6080243648157353
-    -0.5166047365590571	0.7641033353626657	-0.2862677570028208	-0.68254820978656
-  EOS
+# Fabricator(:SP1_f1_plain_text, class_name: OpenStruct) do
+#   name 'SP1_f1'
+#   pcm (<<-EOS).strip_doc
+#     SP1_f1
+#     682.6436366358055  443.1455214015781  2075.655346294993  287.211468117951
+#     299.8883246804867  103.74338315843572  2613.8927022405364  471.1315623708902
+#     591.4892493324709  42.631827541794564  2845.1654083148564  9.36948726124641
+#     7.071084742361592  45.29093411231232  3432.8847704374107  3.409183158303573
+#     91.308984085713  19.1536481364332  3373.656949880137  4.5363903481026
+#     809.2082973387932  2246.941954176211  61.30766021687515  371.19806071846244
+#     120.56476435866055  42.4349244403591  3242.1560628684038  83.50022078295852
+#     13.72524477409959  35.858220519297525  3332.4066864946167  106.66582066236779
+#     558.1188080161639  90.0084504200356  2694.854973210736  145.67374080342415
+#     264.0088462230318  254.7175868081866  2796.88087480315  173.0486646159857
+#     519.46013914282  1874.9349086474765  654.5411208373813  439.7198038226514
+#   EOS
+#   pwm (<<-EOS).strip_doc
+#     SP1_f1
+#     -0.24435707885585292	-0.674823404693731	0.8657012535789866	-1.1060188862599287
+#     -1.0631255752097797	-2.111925969423868	1.0960627561110403	-0.6138563775211977
+#     -0.3872276234760535	-2.9739851913218045	1.1807800242010378	-4.338927525031566
+#     -4.563896055436894	-2.9161633002532277	1.3684371349982638	-5.077972423609655
+#     -2.2369752892820083	-3.7196436313301846	1.3510439136452734	-4.889930670508233
+#     -0.07473964149330865	0.944919654762011	-2.6246857648086044	-0.8510983487822436
+#     -1.9643526491643322	-2.978402770880115	1.3113096718240573	-2.324334259499025
+#     -4.0155484139655835	-3.1384268078096667	1.3387488589788057	-2.084673903537648
+#     -0.44509385828355363	-2.2510053061629702	1.1265431574368685	-1.7780413702431372
+#     -1.1896356092245048	-1.2251832285630027	1.1636760063747527	-1.6080243648157353
+#     -0.5166047365590571	0.7641033353626657	-0.2862677570028208	-0.68254820978656
+#   EOS
   
-  pwm_by_ppm (<<-EOS).strip_doc
-    SP1_f1
-    -0.24500451019749314	-0.6770792648706158	0.8670547406179426	-1.1107587045732945
-    -1.0675673174344313	-2.129057091432141	1.097618374273881	-0.6158400910824666
-    -0.3883339637317867	-3.018376372012639	1.1823990131526274	-4.533519098288315
-    -4.814963574678032	-2.957870589233678	1.3701787559041199	-5.544504752142028
-    -2.256728287148141	-3.818484271031738	1.3527751116079707	-5.258845853421905
-    -0.07492111272663467	0.9463479675413448	-2.6550726738330934	-0.8542416951821531
-    -1.9787903996167093	-3.023005758900076	1.313016367251334	-2.3461281957623594
-    -4.151740650307917	-3.191404627775074	1.340472578885988	-2.1012766959190534
-    -0.44640561441369214	-2.271073912244469	1.1281221968922746	-1.789608002606767
-    -1.1949948607174645	-1.2308220430118417	1.1652826302263302	-1.6174046184238486
-    -0.5181873934002441	0.7653517506909445	-0.2870430604819932	-0.6848397571539165
-  EOS
+#   pwm_by_ppm (<<-EOS).strip_doc
+#     SP1_f1
+#     -0.24500451019749314	-0.6770792648706158	0.8670547406179426	-1.1107587045732945
+#     -1.0675673174344313	-2.129057091432141	1.097618374273881	-0.6158400910824666
+#     -0.3883339637317867	-3.018376372012639	1.1823990131526274	-4.533519098288315
+#     -4.814963574678032	-2.957870589233678	1.3701787559041199	-5.544504752142028
+#     -2.256728287148141	-3.818484271031738	1.3527751116079707	-5.258845853421905
+#     -0.07492111272663467	0.9463479675413448	-2.6550726738330934	-0.8542416951821531
+#     -1.9787903996167093	-3.023005758900076	1.313016367251334	-2.3461281957623594
+#     -4.151740650307917	-3.191404627775074	1.340472578885988	-2.1012766959190534
+#     -0.44640561441369214	-2.271073912244469	1.1281221968922746	-1.789608002606767
+#     -1.1949948607174645	-1.2308220430118417	1.1652826302263302	-1.6174046184238486
+#     -0.5181873934002441	0.7653517506909445	-0.2870430604819932	-0.6848397571539165
+#   EOS
   
-  ppm (<<-EOS).strip_doc
-    SP1_f1
-    0.1956752520244457	0.12702471235371654	0.5949727811186595	0.08232725450317827
-    0.0859609910087678	0.029737349849824683	0.7492549345313109	0.13504672461010295
-    0.1695464539935781	0.012220129436222756	0.8155477154477051	0.002685701122505801
-    0.0020268793478638923	0.012982344624970667	0.9840135563800679	0.0009772196471150077
-    0.0261731121689194	0.005490265674714912	0.9670362960755289	0.0013003260808535316
-    0.2319541690923538	0.6440709464963454	0.017573432491199324	0.10640145192010551
-    0.03455908674020943	0.012163688473573988	0.9293424426115627	0.02393478217466954
-    0.003934250004152571	0.010278520095551809	0.9552121828034635	0.030575047096847708
-    0.15998103923791546	0.025800322855227358	0.7724622302949381	0.04175640761192835
-    0.07567637746682139	0.07301309983548783	0.8017072754923166	0.04960324720538194
-    0.14889978927270572	0.537437604468227	0.1876198530340185	0.1260427532250494
-  EOS
-end
+#   ppm (<<-EOS).strip_doc
+#     SP1_f1
+#     0.1956752520244457	0.12702471235371654	0.5949727811186595	0.08232725450317827
+#     0.0859609910087678	0.029737349849824683	0.7492549345313109	0.13504672461010295
+#     0.1695464539935781	0.012220129436222756	0.8155477154477051	0.002685701122505801
+#     0.0020268793478638923	0.012982344624970667	0.9840135563800679	0.0009772196471150077
+#     0.0261731121689194	0.005490265674714912	0.9670362960755289	0.0013003260808535316
+#     0.2319541690923538	0.6440709464963454	0.017573432491199324	0.10640145192010551
+#     0.03455908674020943	0.012163688473573988	0.9293424426115627	0.02393478217466954
+#     0.003934250004152571	0.010278520095551809	0.9552121828034635	0.030575047096847708
+#     0.15998103923791546	0.025800322855227358	0.7724622302949381	0.04175640761192835
+#     0.07567637746682139	0.07301309983548783	0.8017072754923166	0.04960324720538194
+#     0.14889978927270572	0.537437604468227	0.1876198530340185	0.1260427532250494
+#   EOS
+# end
 
 
-Fabricator(:KLF4_f2_plain_text, class_name: OpenStruct) do
-  name 'KLF4_f2'
+# Fabricator(:KLF4_f2_plain_text, class_name: OpenStruct) do
+#   name 'KLF4_f2'
   
-  pcm (<<-EOS).strip_doc
-    KLF4_f2
-    1233.46088405354  93.18173277811673  1036.6014857092885  1258.2948629970272
-    263.979242343185  5.314520555872139  3347.5949971525274  4.650205486388122
-    76.7700780003465  6.643150694840173  3529.4896409394937  8.636095903292224
-    57.86097393406657  18.102585643439472  3520.3342027139347  25.24120324653207
-    518.1947904009378  1545.9062946905135  22.396758181071043  1535.0411222654507
-    137.98151691820345  9.300410972776241  3456.320530770924  17.936506876068467
-    115.27647661640499  81.51802997128804  1861.9425868567278  1562.801872093553
-    227.8095486111286  42.84555258785854  3278.6396005325996  72.244263806387
-    108.73384179997886  134.47328134862394  3162.880454846513  215.45138754285665
-    238.49636899561344  2225.9561104691043  402.40727964384774  754.6792064294074
-  EOS
+#   pcm (<<-EOS).strip_doc
+#     KLF4_f2
+#     1233.46088405354  93.18173277811673  1036.6014857092885  1258.2948629970272
+#     263.979242343185  5.314520555872139  3347.5949971525274  4.650205486388122
+#     76.7700780003465  6.643150694840173  3529.4896409394937  8.636095903292224
+#     57.86097393406657  18.102585643439472  3520.3342027139347  25.24120324653207
+#     518.1947904009378  1545.9062946905135  22.396758181071043  1535.0411222654507
+#     137.98151691820345  9.300410972776241  3456.320530770924  17.936506876068467
+#     115.27647661640499  81.51802997128804  1861.9425868567278  1562.801872093553
+#     227.8095486111286  42.84555258785854  3278.6396005325996  72.244263806387
+#     108.73384179997886  134.47328134862394  3162.880454846513  215.45138754285665
+#     238.49636899561344  2225.9561104691043  402.40727964384774  754.6792064294074
+#   EOS
 
-  pwm (<<-EOS).strip_doc
-    KLF4_f2
-    0.30861857265872605	-2.254321000121579	0.13505703522674192	0.3285194224375633
-    -1.227018967707036	-4.814127713368663	1.3059890687390967	-4.908681463544344
-    -2.443469374521196	-4.648238485031404	1.3588686548279805	-4.441801801188402
-    -2.7177827948276123	-3.8073538975356565	1.356272809724262	-3.504104725510225
-    -0.5563232977367343	0.5340697765121405	-3.61417723090579	0.5270259776377405
-    -1.8687622060887386	-4.381483976582316	1.337932245336098	-3.815629658877517
-    -2.045671123823928	-2.384975142213679	0.7198551207724355	0.5449254135616948
-    -1.373157530374372	-3.0063112097748217	1.285188335493552	-2.5026044231773543
-    -2.1030513122772208	-1.8941348100402244	1.249265758393991	-1.4284210948906104
-    -1.3277128628152939	0.8982415633049462	-0.8080773665408135	-0.18161647647456935
-  EOS
+#   pwm (<<-EOS).strip_doc
+#     KLF4_f2
+#     0.30861857265872605	-2.254321000121579	0.13505703522674192	0.3285194224375633
+#     -1.227018967707036	-4.814127713368663	1.3059890687390967	-4.908681463544344
+#     -2.443469374521196	-4.648238485031404	1.3588686548279805	-4.441801801188402
+#     -2.7177827948276123	-3.8073538975356565	1.356272809724262	-3.504104725510225
+#     -0.5563232977367343	0.5340697765121405	-3.61417723090579	0.5270259776377405
+#     -1.8687622060887386	-4.381483976582316	1.337932245336098	-3.815629658877517
+#     -2.045671123823928	-2.384975142213679	0.7198551207724355	0.5449254135616948
+#     -1.373157530374372	-3.0063112097748217	1.285188335493552	-2.5026044231773543
+#     -2.1030513122772208	-1.8941348100402244	1.249265758393991	-1.4284210948906104
+#     -1.3277128628152939	0.8982415633049462	-0.8080773665408135	-0.18161647647456935
+#   EOS
 
-  pwm_by_ppm (<<-EOS).strip_doc
-    KLF4_f2
-    0.3092192421596327	-2.2738082797138253	0.13534285704681936	0.32915281813495917
-    -1.2324895093929382	-5.137917180091503	1.307637473739625	-5.271448572716026
-    -2.4675450270943275	-4.914773628777294	1.3605485798774357	-4.652409364309802
-    -2.7503168499566213	-3.9123052006620864	1.3579512260780577	-3.5798822732152016
-    -0.5580087671420197	0.5350056338953667	-3.699443757631887	0.5279524674519223
-    -1.8812402411482916	-4.578301392156081	1.3395998898354127	-3.9215218557670104
-    -2.0610265944380752	-2.4075357595386326	0.7210156412752609	0.5458755791300577
-    -1.3798500151830562	-3.0507581325511492	1.2868238774479581	-2.5283070518025443
-    -2.1194569041801143	-1.906994454335074	1.2508784457678146	-1.435624677710707
-    -1.3340058960845615	0.899581832910703	-0.8108952727718963	-0.18206721514971644
-  EOS
+#   pwm_by_ppm (<<-EOS).strip_doc
+#     KLF4_f2
+#     0.3092192421596327	-2.2738082797138253	0.13534285704681936	0.32915281813495917
+#     -1.2324895093929382	-5.137917180091503	1.307637473739625	-5.271448572716026
+#     -2.4675450270943275	-4.914773628777294	1.3605485798774357	-4.652409364309802
+#     -2.7503168499566213	-3.9123052006620864	1.3579512260780577	-3.5798822732152016
+#     -0.5580087671420197	0.5350056338953667	-3.699443757631887	0.5279524674519223
+#     -1.8812402411482916	-4.578301392156081	1.3395998898354127	-3.9215218557670104
+#     -2.0610265944380752	-2.4075357595386326	0.7210156412752609	0.5458755791300577
+#     -1.3798500151830562	-3.0507581325511492	1.2868238774479581	-2.5283070518025443
+#     -2.1194569041801143	-1.906994454335074	1.2508784457678146	-1.435624677710707
+#     -1.3340058960845615	0.899581832910703	-0.8108952727718963	-0.18206721514971644
+#   EOS
   
-  ppm (<<-EOS).strip_doc
-    KLF4_f2
-    0.3405902561841722	0.025729871655343288	0.28623231603288946	0.34744755612759504
-    0.07289145439416013	0.001467475735162407	0.9243570286024104	0.0012840412682671063
-    0.02119819190981491	0.0018343446689530088	0.9745828153515933	0.002384648069638911
-    0.015976902218825483	0.004998589222896949	0.9720547635170884	0.006969745041189289
-    0.14308690182046985	0.4268644654665126	0.006184320642189763	0.423864312070828
-    0.038100243634326486	0.0025680825365342118	0.9543789432229661	0.004952730606173124
-    0.03183079837421573	0.02250922349503941	0.5141302094426423	0.431529768688103
-    0.06290407221320286	0.011830758413914766	0.9053166710980188	0.019948498274864
-    0.030024208723052264	0.03713152961441303	0.8733525953866614	0.05949166627587335
-    0.06585497802594685	0.6146437002752069	0.11111499378388463	0.20838632791496178
-  EOS
-end
+#   ppm (<<-EOS).strip_doc
+#     KLF4_f2
+#     0.3405902561841722	0.025729871655343288	0.28623231603288946	0.34744755612759504
+#     0.07289145439416013	0.001467475735162407	0.9243570286024104	0.0012840412682671063
+#     0.02119819190981491	0.0018343446689530088	0.9745828153515933	0.002384648069638911
+#     0.015976902218825483	0.004998589222896949	0.9720547635170884	0.006969745041189289
+#     0.14308690182046985	0.4268644654665126	0.006184320642189763	0.423864312070828
+#     0.038100243634326486	0.0025680825365342118	0.9543789432229661	0.004952730606173124
+#     0.03183079837421573	0.02250922349503941	0.5141302094426423	0.431529768688103
+#     0.06290407221320286	0.011830758413914766	0.9053166710980188	0.019948498274864
+#     0.030024208723052264	0.03713152961441303	0.8733525953866614	0.05949166627587335
+#     0.06585497802594685	0.6146437002752069	0.11111499378388463	0.20838632791496178
+#   EOS
+# end