bioinform 0.1.8 → 0.1.9

data/spec/data_models/pm_spec.rb

@@ -3,7 +3,7 @@ require_relative '../../lib/bioinform/data_models/pm'
 
 module Bioinform
   describe PM do
-    {:to_pcm => PCM, :to_pwm => PWM, :to_ppm => PPM}.each do |converter_method, result_klass|
+    {:as_pcm => PCM, :as_pwm => PWM, :as_ppm => PPM}.each do |converter_method, result_klass|
       describe "##{converter_method}" do
         before :each do
           @collection = Collection.new(name: 'Collection 1')
@@ -17,97 +17,97 @@ module Bioinform
         it "should return an instance of #{result_klass}" do
           @conv_motif.should be_kind_of(result_klass)
         end
-        it 'should return have the same matrix, name, background and tags' do
+        it 'should return have the same matrix, name and background' do #, background and tags' do
           @conv_motif.matrix.should == @matrix
           @conv_motif.name.should == @name
           @conv_motif.background.should == @background
-          @conv_motif.tags.should == @tags
+#          @conv_motif.tags.should == @tags
         end
       end
     end
 
-    describe '#tagged?' do
-      context 'when PM marked with Collection object' do
-        context 'without collection-name' do
-          before :each do
-            @marking_collection = Collection.new
-            @nonmarking_collection = Collection.new
-            @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
-            @pm.mark(@marking_collection)
-          end
-          it 'should be true for marking collection' do
-            @pm.should be_tagged(@marking_collection)
-          end
-          it 'should be false for nonmarking collection' do
-            @pm.should_not be_tagged(@nonmarking_collection)
-          end
-          it 'should be false for nil-name' do
-            @pm.should_not be_tagged(nil)
-          end
-          it 'should be false for any string' do
-            @pm.should_not be_tagged('Another name')
-          end
-        end
-        context 'with collection-name' do
-          before :each do
-            @marking_collection = Collection.new(name: 'Collection name')
-            @nonmarking_collection = Collection.new(name: 'Another name')
-            @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
-            @pm.mark(@marking_collection)
-          end
-          it 'should be true for marking collection' do
-            @pm.should be_tagged(@marking_collection)
-          end
-          it 'should be false for nonmarking collection' do
-            @pm.should_not be_tagged(@nonmarking_collection)
-          end
-          it 'should be true for name of marking collection' do
-            @pm.should be_tagged('Collection name')
-          end
-          it 'should be false for string that is not name of marking collection' do
-            @pm.should_not be_tagged('Another name')
-          end
-        end
-      end
+    # describe '#tagged?' do
+      # context 'when PM marked with Collection object' do
+        # context 'without collection-name' do
+          # before :each do
+            # @marking_collection = Collection.new
+            # @nonmarking_collection = Collection.new
+            # @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
+            # @pm.mark(@marking_collection)
+          # end
+          # it 'should be true for marking collection' do
+            # @pm.should be_tagged(@marking_collection)
+          # end
+          # it 'should be false for nonmarking collection' do
+            # @pm.should_not be_tagged(@nonmarking_collection)
+          # end
+          # it 'should be false for nil-name' do
+            # @pm.should_not be_tagged(nil)
+          # end
+          # it 'should be false for any string' do
+            # @pm.should_not be_tagged('Another name')
+          # end
+        # end
+        # context 'with collection-name' do
+          # before :each do
+            # @marking_collection = Collection.new(name: 'Collection name')
+            # @nonmarking_collection = Collection.new(name: 'Another name')
+            # @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
+            # @pm.mark(@marking_collection)
+          # end
+          # it 'should be true for marking collection' do
+            # @pm.should be_tagged(@marking_collection)
+          # end
+          # it 'should be false for nonmarking collection' do
+            # @pm.should_not be_tagged(@nonmarking_collection)
+          # end
+          # it 'should be true for name of marking collection' do
+            # @pm.should be_tagged('Collection name')
+          # end
+          # it 'should be false for string that is not name of marking collection' do
+            # @pm.should_not be_tagged('Another name')
+          # end
+        # end
+      # end
 
-      context 'when PM marked with name' do
-        before :each do
-          @nonmarking_collection = Collection.new(name: 'Another name')
-          @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
-          @pm.mark('Mark name')
-        end
-        it 'should be true for marking name' do
-          @pm.should be_tagged('Mark name')
-        end
-        it 'should be false for string that is not marking name' do
-          @pm.should_not be_tagged('Another name')
-        end
-        it 'should be false for nonmarking collection' do
-          @pm.should_not be_tagged(@nonmarking_collection)
-        end
-      end
+      # context 'when PM marked with name' do
+        # before :each do
+          # @nonmarking_collection = Collection.new(name: 'Another name')
+          # @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
+          # @pm.mark('Mark name')
+        # end
+        # it 'should be true for marking name' do
+          # @pm.should be_tagged('Mark name')
+        # end
+        # it 'should be false for string that is not marking name' do
+          # @pm.should_not be_tagged('Another name')
+        # end
+        # it 'should be false for nonmarking collection' do
+          # @pm.should_not be_tagged(@nonmarking_collection)
+        # end
+      # end
 
-      context 'when PM marked with several marks' do
-        before :each do
-          @collection_1 = Collection.new(name: 'First name')
-          @collection_2 = Collection.new(name: 'Second name')
-          @collection_3 = Collection.new(name: 'Nonmarking collection')
-          @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
-          @pm.mark(@collection_1)
-          @pm.mark(@collection_2)
-          @pm.mark('Stringy-name')
-        end
-        it 'should be true for each mark' do
-          @pm.should be_tagged(@collection_1)
-          @pm.should be_tagged(@collection_2)
-          @pm.should be_tagged('Stringy-name')
-        end
-        it 'should be false for not presented marks' do
-          @pm.should_not be_tagged(@collection_3)
-          @pm.should_not be_tagged('Bad stringy-name')
-        end
-      end
-    end
+      # context 'when PM marked with several marks' do
+        # before :each do
+          # @collection_1 = Collection.new(name: 'First name')
+          # @collection_2 = Collection.new(name: 'Second name')
+          # @collection_3 = Collection.new(name: 'Nonmarking collection')
+          # @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
+          # @pm.mark(@collection_1)
+          # @pm.mark(@collection_2)
+          # @pm.mark('Stringy-name')
+        # end
+        # it 'should be true for each mark' do
+          # @pm.should be_tagged(@collection_1)
+          # @pm.should be_tagged(@collection_2)
+          # @pm.should be_tagged('Stringy-name')
+        # end
+        # it 'should be false for not presented marks' do
+          # @pm.should_not be_tagged(@collection_3)
+          # @pm.should_not be_tagged('Bad stringy-name')
+        # end
+      # end
+    # end
 
     describe '#==' do
       it 'should be true iff motifs have the same matrix, background and name' do
@@ -327,44 +327,6 @@ module Bioinform
       end
     end
 
-    describe '#best_score' do
-      it 'should be equal to best score' do
-        @pm = PM.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]] )
-        @pm.best_score.should == 4.9 + 7.13 + (-1.0)
-      end
-    end
-    describe '#worst_score' do
-      it 'should be equal to worst score' do
-        @pm = PM.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]] )
-        @pm.worst_score.should == 1.3 + 3.25 + (-1.5)
-      end
-    end
-
-    describe '#best_suffix' do
-      it 'should return maximal score of suffices from i-th position inclusively i.e. [i..end]' do
-        @pm = PM.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]] )
-        @pm.best_suffix(0).should == (4.9 + 7.13 - 1.0)
-        @pm.best_suffix(1).should == (7.13 - 1.0)
-        @pm.best_suffix(2).should == (-1.0)
-        @pm.best_suffix(3).should == (0.0)
-      end
-      it 'should give right results after left(right)_augment, discrete, reverse_complement etc' do
-        pm = PM.new([[1, 2, 3, 4], [10,10.5,11,11.5]])
-        pm.best_suffix(1).should == 11.5
-        pm.left_augment!(1)
-        pm.best_suffix(1).should == 15.5
-      end
-    end
-    describe '#worst_suffix' do
-      it 'should return minimal score of suffices from i-th position inclusively i.e. [i..end]' do
-        @pm = PM.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]] )
-        @pm.worst_suffix(0).should == (1.3 + 3.25 - 1.5)
-        @pm.worst_suffix(1).should == (3.25 - 1.5)
-        @pm.worst_suffix(2).should == (- 1.5)
-        @pm.worst_suffix(3).should == (0.0)
-      end
-    end
-
     [:reverse_complement].each do |meth|
       describe "nonbang method #{meth}" do
         before :each do

data/spec/data_models/pwm_spec.rb

@@ -37,5 +37,43 @@ module Bioinform
       end
     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
+    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
+    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
+    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
+    end
+
   end
 end

data/spec/fabricators/collection_fabricator.rb

@@ -1,6 +1,6 @@
-Fabricator(:pm_collection, from: Bioinform::Collection, aliases: [:two_elements_collection]) do
+Fabricator(:three_elements_collection, class_name: Bioinform::Collection, aliases: [:pm_collection]) do
   name 'PM_collection'
-  after_build{|collection| collection << Fabricate(:pm_first) << Fabricate(:pm_second) }
+  after_build{|collection| collection << Fabricate(:pm_1) << Fabricate(:pm_2) << Fabricate(:pm_3) }
 end
 
 Fabricator(:unnamed_pm_collection, from: :pm_collection) do

data/spec/fabricators/motif_fabricator.rb

@@ -0,0 +1,33 @@
+Fabricator(:motif, class_name: Bioinform::Motif) do
+end
+
+Fabricator(:motif_with_name, from: :motif) do
+  name 'Motif name'
+end
+
+Fabricator(:motif_pcm, from: :motif) do
+  pcm(fabricator: :pcm)
+end
+
+Fabricator(:motif_pwm, from: :motif) do
+  pwm(fabricator: :pwm)
+end
+
+Fabricator(:motif_ppm, from: :motif) do
+  ppm(fabricator: :ppm)
+end
+
+Fabricator(:motif_pcm_and_ppm, from: :motif) do
+  pcm(fabricator: :pcm)
+  ppm(fabricator: :ppm)
+end
+
+Fabricator(:motif_pwm_and_ppm, from: :motif) do
+  pwm(fabricator: :pwm)
+  ppm(fabricator: :ppm)
+end
+
+Fabricator(:motif_pcm_and_pwm, from: :motif) do
+  pcm(fabricator: :pcm)
+  pwm(fabricator: :pwm)
+end

data/spec/fabricators/motif_formats_fabricator.rb

@@ -0,0 +1,125 @@
+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
+  
+  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
+
+
+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
+
+  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
+  
+  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

data/spec/fabricators/pcm_fabricator.rb

@@ -0,0 +1,25 @@
+Fabricator(:pcm, class_name: Bioinform::PCM) do
+  initialize_with{ Bioinform::PCM.new(matrix: [[1, 2, 3, 1],[4, 0, 1, 2]], name: 'PCM_name') }
+end
+
+Fabricator(:pcm_with_floats, from: :pcm) do
+  matrix [[1, 2.3, 3.2, 1],[4.4, 0.1, 0.9, 2.1]]
+end
+
+Fabricator(:completely_different_pcm, from: :pcm) do
+  matrix [[101,207,138,248],[85,541,7,61]]
+  name 'PCM_another_name'
+end
+
+Fabricator(:pcm_1, from: :pcm) do
+  matrix [[7,10,2,3],[4,5,6,7]]
+  name 'motif_1'
+end
+Fabricator(:pcm_2, from: :pcm) do
+  matrix [[5,7,4,6],[11,6,2,3],[10,3,3,6]]
+  name 'motif_2'
+end
+Fabricator(:pcm_3, from: :pcm) do
+  matrix [[3,4,1,14],[9,2,9,2]]
+  name 'motif_3'
+end