bioinform 0.1.12 → 0.1.13

data/spec/data_models/motif_spec.rb

@@ -1,224 +1,224 @@
-require_relative '../../lib/bioinform/data_models/motif'
-
-shared_examples 'when pm is PM' do
-  context 'when pm-value is a PCM' do
-    let(:pm) { Fabricate(:pcm) }
-    it 'sets pcm-attribute to specified PM' do
-      subject.pcm.should == Fabricate(:pcm)
-    end
-  end
-  context 'when pm-value is a PWM' do
-    let(:pm) { Fabricate(:pwm) }
-    it 'sets pwm-attribute to specified PM' do
-      subject.pwm.should == Fabricate(:pwm)
-    end
-  end
-  context 'when pm-value is a PPM' do
-    let(:pm) { Fabricate(:ppm) }
-    it 'sets ppm-attribute to specified PM' do
-      subject.ppm.should == Fabricate(:ppm)
-    end
-  end
-  context 'when pm-value is a PM' do
-    let(:pm) { Fabricate(:pm) }
-    it 'sets only parameter pm attribute to specified PM' do
-      subject.parameters.pm.should == Fabricate(:pm)
-      subject.pcm.should be_nil
-      subject.pwm.should be_nil
-      subject.ppm.should be_nil
-    end
-  end
-end
-
-
-module Bioinform
-  describe Motif do
-    describe '.new' do
-      it 'accepts empty argument list' do
-        expect{ described_class.new }.to_not raise_error
-      end
-
-      context 'when argument is a Hash' do
-        subject{ described_class.new(hash) }
-        context 'which contains usual symbolic parameters' do
-          let(:hash){ {:a => 123, :key => 'value', :threshold => {0.1 => 15} } }
-          it 'sets its content as parameters' do
-            subject.parameters.a.should == 123
-            subject.parameters.key.should == 'value'
-            subject.parameters.threshold.should == {0.1 => 15}
-          end
-        end
-        context 'which contains any combination of :pwm, :pcm and :ppm keys' do
-          let(:hash) { {pcm: 'my_pcm', ppm: 'my_ppm'} }
-          it 'sets corresponding attributes to specified values' do
-            subject.pcm.should == 'my_pcm'
-            subject.ppm.should == 'my_ppm'
-          end
-        end
-      end
-
-      context 'when argument is a Hash with pm-key' do
-        subject{ described_class.new(pm: pm) }
-
-        include_examples 'when pm is PM'
-
-        context 'when pm-value is a usual object' do
-          let(:pm) { 'stub pm' }
-          it 'sets only parameter pm attribute to specified value' do
-            subject.parameters.pm.should == 'stub pm'
-            subject.pcm.should be_nil
-            subject.pwm.should be_nil
-            subject.ppm.should be_nil
-          end
-        end
-      end
-      context 'when argument is neither PM nor Hash' do
-        it 'raises ArgumentError' do
-          expect{ described_class.new('stub pm') }.to raise_error(ArgumentError)
-        end
-      end
-    end
-
-    ########################################################
-    describe '#pcm' do
-      subject {  motif.pcm }
-      context 'when pcm is set' do
-        context 'when pwm and ppm aren\'t setted' do
-          let(:motif) { Fabricate(:motif_pcm) }
-          it 'returns setted pcm' do
-            subject.should == Fabricate(:pcm)
-          end
-        end
-        context 'when ppm also setted' do
-          let(:motif) { Fabricate(:motif_pcm_and_ppm) }
-          it 'returns setted pcm' do
-            subject.should == Fabricate(:pcm)
-          end
-        end
-        context 'when pwm also setted' do
-          let(:motif) { Fabricate(:motif_pcm_and_pwm) }
-          it 'returns setted pcm' do
-            subject.should == Fabricate(:pcm)
-          end
-        end
-      end
-
-      context 'when pcm isn\'t set' do
-        context 'when nothing set' do
-          let(:motif) { Fabricate(:motif) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-        context 'when pwm setted' do
-          let(:motif) { Fabricate(:motif_pwm) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-        context 'when ppm setted' do
-          let(:motif) { Fabricate(:motif_ppm) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-      end
-    end
-    ############################################
-    describe '#pwm' do
-      subject {  motif.pwm }
-      context 'when pwm is set' do
-        context 'when pcm and ppm aren\'t setted' do
-          let(:motif) { Fabricate(:motif_pwm) }
-          it 'returns setted pwm' do
-            subject.should == Fabricate(:pwm)
-          end
-        end
-        context 'when ppm also setted' do
-          let(:motif) { Fabricate(:motif_pwm_and_ppm) }
-          it 'returns setted pwm' do
-            subject.should == Fabricate(:pwm)
-          end
-        end
-        context 'when pcm also setted' do
-          let(:motif) { Fabricate(:motif_pcm_and_pwm) }
-          it 'returns setted pwm' do
-            subject.should == Fabricate(:pwm)
-          end
-        end
-      end
-
-      context 'when pwm isn\'t set' do
-        context 'when nothing set' do
-          let(:motif) { Fabricate(:motif) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-        context 'when pcm setted' do
-          let(:motif) { Fabricate(:motif_pcm) }
-          it 'returns pcm converted to pwm' do
-            subject.should == Fabricate(:pwm_by_pcm)
-          end
-        end
-        context 'when ppm setted' do
-          let(:motif) { Fabricate(:motif_ppm) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-      end
-    end
-
-    ############################################
-    describe '#ppm' do
-      subject {  motif.ppm }
-      context 'when ppm is set' do
-        context 'when pcm and pwm aren\'t setted' do
-          let(:motif) { Fabricate(:motif_ppm) }
-          it 'returns setted ppm' do
-            subject.should == Fabricate(:ppm)
-          end
-        end
-        context 'when pcm also setted' do
-          let(:motif) { Fabricate(:motif_pcm_and_ppm) }
-          it 'returns setted ppm' do
-            subject.should == Fabricate(:ppm)
-          end
-        end
-        context 'when pwm also setted' do
-          let(:motif) { Fabricate(:motif_pwm_and_ppm) }
-          it 'returns setted ppm' do
-            subject.should == Fabricate(:ppm)
-          end
-        end
-      end
-
-      context 'when ppm isn\'t set' do
-        context 'when nothing set' do
-          let(:motif) { Fabricate(:motif) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-        context 'when pcm setted' do
-          let(:motif) { Fabricate(:motif_pcm) }
-          it 'returns pcm converted to ppm' do
-            subject.should == Fabricate(:ppm_by_pcm)
-          end
-        end
-        context 'when pwm setted' do
-          let(:motif) { Fabricate(:motif_pwm) }
-          it 'returns nil' do
-            subject.should be_nil
-          end
-        end
-      end
-    end
-
-
-
-
-
-  end
+require_relative '../../lib/bioinform/data_models/motif'
+
+shared_examples 'when pm is PM' do
+  context 'when pm-value is a PCM' do
+    let(:pm) { Fabricate(:pcm) }
+    it 'sets pcm-attribute to specified PM' do
+      subject.pcm.should == Fabricate(:pcm)
+    end
+  end
+  context 'when pm-value is a PWM' do
+    let(:pm) { Fabricate(:pwm) }
+    it 'sets pwm-attribute to specified PM' do
+      subject.pwm.should == Fabricate(:pwm)
+    end
+  end
+  context 'when pm-value is a PPM' do
+    let(:pm) { Fabricate(:ppm) }
+    it 'sets ppm-attribute to specified PM' do
+      subject.ppm.should == Fabricate(:ppm)
+    end
+  end
+  context 'when pm-value is a PM' do
+    let(:pm) { Fabricate(:pm) }
+    it 'sets only parameter pm attribute to specified PM' do
+      subject.parameters.pm.should == Fabricate(:pm)
+      subject.pcm.should be_nil
+      subject.pwm.should be_nil
+      subject.ppm.should be_nil
+    end
+  end
+end
+
+
+module Bioinform
+  describe Motif do
+    describe '.new' do
+      it 'accepts empty argument list' do
+        expect{ described_class.new }.to_not raise_error
+      end
+
+      context 'when argument is a Hash' do
+        subject{ described_class.new(hash) }
+        context 'which contains usual symbolic parameters' do
+          let(:hash){ {:a => 123, :key => 'value', :threshold => {0.1 => 15} } }
+          it 'sets its content as parameters' do
+            subject.parameters.a.should == 123
+            subject.parameters.key.should == 'value'
+            subject.parameters.threshold.should == {0.1 => 15}
+          end
+        end
+        context 'which contains any combination of :pwm, :pcm and :ppm keys' do
+          let(:hash) { {pcm: 'my_pcm', ppm: 'my_ppm'} }
+          it 'sets corresponding attributes to specified values' do
+            subject.pcm.should == 'my_pcm'
+            subject.ppm.should == 'my_ppm'
+          end
+        end
+      end
+
+      context 'when argument is a Hash with pm-key' do
+        subject{ described_class.new(pm: pm) }
+
+        include_examples 'when pm is PM'
+
+        context 'when pm-value is a usual object' do
+          let(:pm) { 'stub pm' }
+          it 'sets only parameter pm attribute to specified value' do
+            subject.parameters.pm.should == 'stub pm'
+            subject.pcm.should be_nil
+            subject.pwm.should be_nil
+            subject.ppm.should be_nil
+          end
+        end
+      end
+      context 'when argument is neither PM nor Hash' do
+        it 'raises ArgumentError' do
+          expect{ described_class.new('stub pm') }.to raise_error(ArgumentError)
+        end
+      end
+    end
+
+    ########################################################
+    describe '#pcm' do
+      subject {  motif.pcm }
+      context 'when pcm is set' do
+        context 'when pwm and ppm aren\'t setted' do
+          let(:motif) { Fabricate(:motif_pcm) }
+          it 'returns setted pcm' do
+            subject.should == Fabricate(:pcm)
+          end
+        end
+        context 'when ppm also setted' do
+          let(:motif) { Fabricate(:motif_pcm_and_ppm) }
+          it 'returns setted pcm' do
+            subject.should == Fabricate(:pcm)
+          end
+        end
+        context 'when pwm also setted' do
+          let(:motif) { Fabricate(:motif_pcm_and_pwm) }
+          it 'returns setted pcm' do
+            subject.should == Fabricate(:pcm)
+          end
+        end
+      end
+
+      context 'when pcm isn\'t set' do
+        context 'when nothing set' do
+          let(:motif) { Fabricate(:motif) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+        context 'when pwm setted' do
+          let(:motif) { Fabricate(:motif_pwm) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+        context 'when ppm setted' do
+          let(:motif) { Fabricate(:motif_ppm) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+      end
+    end
+    ############################################
+    describe '#pwm' do
+      subject {  motif.pwm }
+      context 'when pwm is set' do
+        context 'when pcm and ppm aren\'t setted' do
+          let(:motif) { Fabricate(:motif_pwm) }
+          it 'returns setted pwm' do
+            subject.should == Fabricate(:pwm)
+          end
+        end
+        context 'when ppm also setted' do
+          let(:motif) { Fabricate(:motif_pwm_and_ppm) }
+          it 'returns setted pwm' do
+            subject.should == Fabricate(:pwm)
+          end
+        end
+        context 'when pcm also setted' do
+          let(:motif) { Fabricate(:motif_pcm_and_pwm) }
+          it 'returns setted pwm' do
+            subject.should == Fabricate(:pwm)
+          end
+        end
+      end
+
+      context 'when pwm isn\'t set' do
+        context 'when nothing set' do
+          let(:motif) { Fabricate(:motif) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+        context 'when pcm setted' do
+          let(:motif) { Fabricate(:motif_pcm) }
+          it 'returns pcm converted to pwm' do
+            subject.should == Fabricate(:pwm_by_pcm)
+          end
+        end
+        context 'when ppm setted' do
+          let(:motif) { Fabricate(:motif_ppm) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+      end
+    end
+
+    ############################################
+    describe '#ppm' do
+      subject {  motif.ppm }
+      context 'when ppm is set' do
+        context 'when pcm and pwm aren\'t setted' do
+          let(:motif) { Fabricate(:motif_ppm) }
+          it 'returns setted ppm' do
+            subject.should == Fabricate(:ppm)
+          end
+        end
+        context 'when pcm also setted' do
+          let(:motif) { Fabricate(:motif_pcm_and_ppm) }
+          it 'returns setted ppm' do
+            subject.should == Fabricate(:ppm)
+          end
+        end
+        context 'when pwm also setted' do
+          let(:motif) { Fabricate(:motif_pwm_and_ppm) }
+          it 'returns setted ppm' do
+            subject.should == Fabricate(:ppm)
+          end
+        end
+      end
+
+      context 'when ppm isn\'t set' do
+        context 'when nothing set' do
+          let(:motif) { Fabricate(:motif) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+        context 'when pcm setted' do
+          let(:motif) { Fabricate(:motif_pcm) }
+          it 'returns pcm converted to ppm' do
+            subject.should == Fabricate(:ppm_by_pcm)
+          end
+        end
+        context 'when pwm setted' do
+          let(:motif) { Fabricate(:motif_pwm) }
+          it 'returns nil' do
+            subject.should be_nil
+          end
+        end
+      end
+    end
+
+
+
+
+
+  end
 end

data/spec/data_models/pcm_spec.rb

@@ -1,56 +1,56 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/data_models/pcm'
-
-module Bioinform
-  describe PCM do
-    describe '#count' do
-      it 'should be equal to sum of elements at position' do
-        Fabricate(:pcm).count.should == 7
-        Fabricate(:pcm_with_floats).count.should == 7.5
-      end
-    end
-
-    describe '#to_pwm' do
-      subject{ Fabricate(:pcm) }
-      it 'should return PWM' do
-        Fabricate(:pcm).to_pwm.should be_kind_of(PWM)
-      end
-      it 'should make transformation: el --> log( (el + p_i*pseudocount) / (p_i*(count + pseudocount)) )' do
-        subject.to_pwm(1).matrix.map{|line|line.map{|el| el.round(3)}}.should == Fabricate(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_1).matrix
-        subject.to_pwm(10).matrix.map{|line|line.map{|el| el.round(3)}}.should == Fabricate(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_10).matrix
-      end
-      it 'should use default pseudocount equal to log(count)' do
-        Fabricate(:pcm).to_pwm.should == Fabricate(:pcm).to_pwm(Math.log(7))
-      end
-      it 'should preserve name' do
-        Fabricate(:pcm, name: nil).to_pwm.name.should be_nil
-        Fabricate(:pcm, name: 'Stub name').to_pwm.name.should == 'Stub name'
-      end
-    end
-
-    describe '#to_ppm' do
-      let(:pcm_motif) { Fabricate(:pcm) }
-      context 'returned object' do
-        subject{ pcm_motif.to_ppm }
-        it { should be_kind_of(PPM)}
-        it 'should have matrix transformed with el --> el / count' do
-          subject.matrix.should == Fabricate(:ppm_pcm_divided_by_count).matrix
-        end
-        context 'when source PCM name is absent' do
-          let(:pcm_motif) { Fabricate(:pcm, name: nil) }
-          it 'should have no name' do
-            subject.name.should be_nil
-          end
-        end
-        context 'when source PCM has name' do
-          let(:pcm_motif) { Fabricate(:pcm, name: 'Stub-name') }
-          it 'should has the same name' do
-            subject.name.should == 'Stub-name'
-          end
-        end
-      end
-    end
-
-
-  end
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/pcm'
+
+module Bioinform
+  describe PCM do
+    describe '#count' do
+      it 'should be equal to sum of elements at position' do
+        Fabricate(:pcm).count.should == 7
+        Fabricate(:pcm_with_floats).count.should == 7.5
+      end
+    end
+
+    describe '#to_pwm' do
+      subject{ Fabricate(:pcm) }
+      it 'should return PWM' do
+        Fabricate(:pcm).to_pwm.should be_kind_of(PWM)
+      end
+      it 'should make transformation: el --> log( (el + p_i*pseudocount) / (p_i*(count + pseudocount)) )' do
+        subject.to_pwm(1).matrix.map{|line|line.map{|el| el.round(3)}}.should == Fabricate(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_1).matrix
+        subject.to_pwm(10).matrix.map{|line|line.map{|el| el.round(3)}}.should == Fabricate(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_10).matrix
+      end
+      it 'should use default pseudocount equal to log(count)' do
+        Fabricate(:pcm).to_pwm.should == Fabricate(:pcm).to_pwm(Math.log(7))
+      end
+      it 'should preserve name' do
+        Fabricate(:pcm, name: nil).to_pwm.name.should be_nil
+        Fabricate(:pcm, name: 'Stub name').to_pwm.name.should == 'Stub name'
+      end
+    end
+
+    describe '#to_ppm' do
+      let(:pcm_motif) { Fabricate(:pcm) }
+      context 'returned object' do
+        subject{ pcm_motif.to_ppm }
+        it { should be_kind_of(PPM)}
+        it 'should have matrix transformed with el --> el / count' do
+          subject.matrix.should == Fabricate(:ppm_pcm_divided_by_count).matrix
+        end
+        context 'when source PCM name is absent' do
+          let(:pcm_motif) { Fabricate(:pcm, name: nil) }
+          it 'should have no name' do
+            subject.name.should be_nil
+          end
+        end
+        context 'when source PCM has name' do
+          let(:pcm_motif) { Fabricate(:pcm, name: 'Stub-name') }
+          it 'should has the same name' do
+            subject.name.should == 'Stub-name'
+          end
+        end
+      end
+    end
+
+
+  end
 end