bioinform 0.1.17 → 0.2.0

data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm

@@ -1,14 +0,0 @@
-GABPA_f1
--0.1106670158341858	0.013801606113892391	0.6054596108973699	-1.3518085041421573
-0.37030668921643345	0.15761121480429963	0.009069314183831202	-0.9888619717703562
-0.47526546359546684	-0.3011678534572083	0.4031522994412777	-1.8638752827041059
--1.5544255540164373	1.1082369687811506	-0.2814091552834454	-5.30708531823271
--0.6362037835776368	1.235338189985594	-3.5801322928552253	-5.717323067092849
--5.852906870733575	-5.852906870733575	1.3841383838057746	-5.852906870733575
--5.852906870733575	-5.852906870733575	1.3841383838057746	-5.852906870733575
-1.3835219739184708	-5.2341956006430985	-5.852906870733575	-5.852906870733575
-1.3756340514956562	-5.394962755562375	-5.394962755562375	-3.401117964959733
--1.2176198315414444	-3.109079898175411	1.2964067931472216	-5.717323067092849
--1.3716559438167257	-0.2761401935045069	-1.8504445165866068	1.0404320473626856
--0.5440863133031895	-0.48103682561971345	0.907381908447086	-1.1280642594012078
-0.10557340209290218	-0.01814819455289191	0.4381106695354074	-1.0304105539540915

data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm

@@ -1,11 +0,0 @@
-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

data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm

@@ -1,12 +0,0 @@
-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

data/spec/cli/data/split_motifs/collection.yaml

@@ -1,188 +0,0 @@
---- !ruby/object:Bioinform::Collection
-container:
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pwm
-      :pwm: !ruby/object:Bioinform::PWM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: GABPA_f1
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - -0.1106670158341858
-          - 0.013801606113892391
-          - 0.6054596108973699
-          - -1.3518085041421573
-        - - 0.37030668921643345
-          - 0.15761121480429963
-          - 0.009069314183831202
-          - -0.9888619717703562
-        - - 0.47526546359546684
-          - -0.3011678534572083
-          - 0.4031522994412777
-          - -1.8638752827041059
-        - - -1.5544255540164373
-          - 1.1082369687811506
-          - -0.2814091552834454
-          - -5.30708531823271
-        - - -0.6362037835776368
-          - 1.235338189985594
-          - -3.5801322928552253
-          - -5.717323067092849
-        - - -5.852906870733575
-          - -5.852906870733575
-          - 1.3841383838057746
-          - -5.852906870733575
-        - - -5.852906870733575
-          - -5.852906870733575
-          - 1.3841383838057746
-          - -5.852906870733575
-        - - 1.3835219739184708
-          - -5.2341956006430985
-          - -5.852906870733575
-          - -5.852906870733575
-        - - 1.3756340514956562
-          - -5.394962755562375
-          - -5.394962755562375
-          - -3.401117964959733
-        - - -1.2176198315414444
-          - -3.109079898175411
-          - 1.2964067931472216
-          - -5.717323067092849
-        - - -1.3716559438167257
-          - -0.2761401935045069
-          - -1.8504445165866068
-          - 1.0404320473626856
-        - - -0.5440863133031895
-          - -0.48103682561971345
-          - 0.907381908447086
-          - -1.1280642594012078
-        - - 0.10557340209290218
-          - -0.01814819455289191
-          - 0.4381106695354074
-          - -1.0304105539540915
-    modifiable: true
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pwm
-      :pwm: !ruby/object:Bioinform::PWM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: KLF4_f2
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - 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
-    modifiable: true
-- !ruby/object:Bioinform::Motif
-  parameters: !ruby/object:OpenStruct
-    table:
-      :original_data_model: :pwm
-      :pwm: !ruby/object:Bioinform::PWM
-        parameters: !ruby/object:OpenStruct
-          table:
-            :name: SP1_f1
-            :background:
-            - 1
-            - 1
-            - 1
-            - 1
-          modifiable: true
-        matrix:
-        - - -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
-    modifiable: true
-parameters: !ruby/object:OpenStruct
-  table: {}

data/spec/cli/merge_into_collection_spec.rb

@@ -1,100 +0,0 @@
-require 'shellwords'
-require 'yaml'
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/cli/merge_into_collection'
-require_relative '../../lib/bioinform/data_models/collection'
-
-
-def run_merge_into_collection(cmd)
-  Bioinform::CLI::MergeIntoCollection.main(cmd.shellsplit)
-end
-
-describe Bioinform::CLI::MergeIntoCollection do
-  before :each do
-    @start_dir = Dir.pwd
-    Dir.chdir File.join(File.dirname(__FILE__), 'data', 'merge_into_collection')
-  end
-  after :each do
-    File.delete('collection.yaml')  if File.exist?('collection.yaml')
-    File.delete('collection.txt')  if File.exist?('collection.txt')
-    File.delete('my_collection.yaml')  if File.exist?('my_collection.yaml')
-    File.delete('my_collection.txt')  if File.exist?('my_collection.txt')
-    File.delete('result.out')  if File.exist?('result.out')
-    Dir.chdir(@start_dir)
-  end
-
-  context 'without --plain option' do
-    context 'when name not specified' do
-      it 'collects motifs into file collection.yaml' do
-        run_merge_into_collection('GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('collection.yaml').should be_true
-        YAML.load(File.read('collection.yaml')).should == YAML.load(File.read('collection.yaml.result'))
-      end
-    end
-    
-    context 'when name specified' do
-      it 'collects motifs into file <collection name>.yaml' do
-        run_merge_into_collection('--name my_collection GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('my_collection.yaml').should be_true
-        YAML.load(File.read('my_collection.yaml')).should == YAML.load(File.read('collection.yaml.result')).set_parameters(name: 'my_collection')
-      end
-    end
-    
-    context 'with --data-model option' do
-      it 'treat motifs as specified data model' do
-        run_merge_into_collection('--data-model pwm GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('collection.yaml').should be_true
-        YAML.load(File.read('collection.yaml')).should == YAML.load(File.read('collection_pwm.yaml.result'))
-      end
-    end
-  end
-  
-  context 'with --plain option' do
-    context 'when name not specified' do
-      it 'should collect motifs into file collection.txt in plain-text format' do
-        run_merge_into_collection('--plain GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('collection.txt').should be_true
-        YAML.load(File.read('collection.txt')).should == YAML.load(File.read('collection.txt.result'))
-      end
-    end
-    
-    context 'when name specified' do
-      it 'should collect motifs into file <collection name>.txt in plain-text format' do
-        run_merge_into_collection('--name my_collection --plain GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('my_collection.txt').should be_true
-        YAML.load(File.read('my_collection.txt')).should == YAML.load(File.read('collection.txt.result'))
-      end
-    end
-
-    context 'with --data-model option' do
-      it 'generate usual txt file' do
-        run_merge_into_collection('--data-model pwm --plain GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-        File.exist?('collection.txt').should be_true
-        YAML.load(File.read('collection.txt')).should == YAML.load(File.read('collection.txt.result'))
-      end
-    end
-  end
-
-  context 'when --output-file specified' do
-    it 'collects motifs into specified file' do
-      run_merge_into_collection('--output-file result.out GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm')
-      File.exist?('result.out').should be_true
-      YAML.load(File.read('result.out')).should == YAML.load(File.read('collection.yaml.result'))
-    end
-  end
-  
-  context 'when filelist is empty' do
-    it 'takes filelist from stdin' do
-      provide_stdin('GABPA_f1.pwm KLF4_f2.pwm SP1_f1.pwm'){ run_merge_into_collection('') }
-      File.exist?('collection.yaml').should be_true
-      YAML.load(File.read('collection.yaml')).should == YAML.load(File.read('collection.yaml.result'))
-    end
-  end
-  context 'when filelist contain folder name' do
-    it 'takes filelist as files from folder' do
-      run_merge_into_collection('pwm_folder')
-      File.exist?('collection.yaml').should be_true
-      YAML.load(File.read('collection.yaml')).should == YAML.load(File.read('collection.yaml.result'))
-    end
-  end
-end

data/spec/data_models/collection_spec.rb

@@ -1,98 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/data_models/collection'
-
-module Bioinform
-  describe Collection do
-    before :each do
-      @collection = Collection.new(name: 'Main collection')
-      @pm_1 = Fabricate(:pm_1)
-      @pm_2 = Fabricate(:pm_2)
-      @pm_3 = Fabricate(:pm_3)
-    end
-    describe '#size' do
-      it 'should return size of collection' do
-        @collection << @pm_1 << @pm_2 << @pm_3
-        @collection.size.should == 3
-      end
-    end
-    describe '#<<' do
-      it 'should add element to collection' do
-        @collection << @pm_1
-        @collection << @pm_2
-        @collection << @pm_3
-        @collection.should include(Motif.new(pm: @pm_1), Motif.new(pm: @pm_2), Motif.new(pm: @pm_3))
-      end
-      it 'should be chainable' do
-        @collection << @pm_1 << @pm_2 << @pm_3
-        @collection.should include(Motif.new(pm: @pm_1), Motif.new(pm: @pm_2), Motif.new(pm: @pm_3))
-      end
-#      it 'should mark motif with name' do
-#        @collection << @pm_1 << @pm_2
-#        @pm_1.should be_tagged('Main collection')
-#        @pm_2.should be_tagged('Main collection')
-#      end
-#      it 'should mark motif with self' do
-#        @collection << @pm_1 << @pm_2
-#        @pm_1.should be_tagged(@collection)
-#        @pm_2.should be_tagged(@collection)
-#      end
-    end
-
-    describe '#each' do
-      before :each do
-        @collection << @pm_1 << @pm_2 << @pm_3
-      end
-      context 'with block given' do
-        it 'should yield Motifs' do
-          expect{|b| @collection.each(&b)}.to yield_successive_args(Motif,Motif,Motif)
-        end
-      end
-      context 'with block given' do
-        it 'return an Enumerator' do
-          @collection.each.should be_kind_of(Enumerator)
-        end
-      end
-    end
-
-    describe '#each(:pcm)' do
-      before :each do
-        @collection << @pm_1.as_pcm << @pm_2 << @pm_3.as_pcm
-      end
-      context 'with block given' do
-        it 'should yield elements of collecton converted to pcm' do
-          expect{|b| @collection.each(:pcm, &b)}.to yield_successive_args(PCM, nil, PCM)
-        end
-      end
-      context 'with block given' do
-        it 'return an Enumerator' do
-          @collection.each(:pcm).should be_kind_of(Enumerator)
-        end
-      end
-    end
-
-    describe '#+' do
-      before :each do
-        @collection << @pm_1 << @pm_2 << @pm_3
-        @pm_sec_1 = Fabricate(:pm_4)
-        @pm_sec_2 = Fabricate(:pm_5)
-        @secondary_collection = Collection.new(name: 'Secondary collection')
-        @secondary_collection << @pm_sec_1 << @pm_sec_2
-        @summary_collection = @collection + @secondary_collection
-      end
-      it 'should create a collection consisting of all elements of both collections' do
-        @summary_collection.should be_kind_of(Collection)
-        @summary_collection.size.should == (@collection.size + @secondary_collection.size)
-        @summary_collection.should include(Motif.new(pm: @pm_1), Motif.new(pm: @pm_2), Motif.new(pm: @pm_3), 
-                                          Motif.new(pm: @pm_sec_1), Motif.new(pm: @pm_sec_2))
-      end
-      # it 'should leave marks on motifs' do
-        # @pm_1.should be_tagged('Main collection')
-        # @pm_sec_1.should be_tagged('Secondary collection')
-      # end
-      # it 'should not mix marks of motifs in different collections' do
-        # @pm_1.should_not be_tagged('Secondary collection')
-        # @pm_sec_1.should_not be_tagged('Main collection')
-      # end
-    end
-  end
-end

data/spec/data_models/motif_spec.rb

@@ -1,224 +0,0 @@
-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