bioinform 0.1.7 → 0.1.8

data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result

@@ -0,0 +1,12 @@
+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/GABPA_f1.mat.result

@@ -0,0 +1,14 @@
+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/split_motifs/KLF4_f2.mat.result

@@ -0,0 +1,11 @@
+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/split_motifs/SP1_f1.mat.result

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

@@ -0,0 +1,197 @@
+--- &14005248 !ruby/object:Bioinform::Collection
+collection:
+- - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: GABPA_f1
+        :tags:
+        - *14005248
+        :background: &14005452
+        - 1
+        - 1
+        - 1
+        - 1
+        :max_hash_size: 1000000
+      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
+  - !ruby/object:OpenStruct
+    table:
+      :rough:
+        0.0005: 12.1
+      :precise:
+        0.0005: 4.51
+- - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: KLF4_f2
+        :tags:
+        - *14005248
+        :background: *14005452
+        :max_hash_size: 1000000
+      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
+  - !ruby/object:OpenStruct
+    table:
+      :rough:
+        0.0005: 11.1
+      :precise:
+        0.0005: 5.8100000000000005
+- - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: SP1_f1
+        :tags:
+        - *14005248
+        :background: *14005452
+        :max_hash_size: 1000000
+      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
+  - !ruby/object:OpenStruct
+    table:
+      :rough:
+        0.0005: 11.1
+      :precise:
+        0.0005: 5.61
+parameters: !ruby/object:OpenStruct
+  table:
+    :rough_discretization: 1
+    :precise_discretization: 10
+    :background: *14005452
+    :pvalues:
+    - 0.0005

data/spec/cli/data/split_motifs/plain_collection.txt

@@ -0,0 +1,38 @@
+> 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
+
+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 
+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/merge_into_collection_spec.rb

@@ -0,0 +1,100 @@
+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/cli/pcm2pwm_spec.rb

@@ -1,6 +1,6 @@
-require 'spec_helper'
 require 'shellwords'
-require 'bioinform/cli/pcm2pwm'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/cli/pcm2pwm'
 
 
 def run_pcm2pwm(cmd)
@@ -10,7 +10,7 @@ end
 describe Bioinform::CLI::PCM2PWM do
   before :each do
     @start_dir = Dir.pwd
-    Dir.chdir File.join(File.dirname(__FILE__), 'data')
+    Dir.chdir File.join(File.dirname(__FILE__), 'data', 'pcm2pwm')
   end
   after :each do
     File.delete('KLF4_f2.pwm')  if File.exist?('KLF4_f2.pwm')

data/spec/cli/split_motifs_spec.rb

@@ -1,6 +1,77 @@
-require 'spec_helper'
-require 'bioinform/cli/split_motifs'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/cli/split_motifs'
 
-describe Bioinform::CLI::SplitMotifs do
+def run_split_motifs(cmd)
+  Bioinform::CLI::SplitMotifs.main(cmd.shellsplit)
+end
 
+describe Bioinform::CLI::SplitMotifs do
+  before :each do
+    @start_dir = Dir.pwd
+    @motifs_in_collection = %w[KLF4_f2 SP1_f1 GABPA_f1]
+    Dir.chdir File.join(File.dirname(__FILE__), 'data', 'split_motifs')
+  end
+  after :each do
+    @motifs_in_collection.each do |motif_name|
+      File.delete("#{motif_name}.mat")  if File.exist?("#{motif_name}.mat")
+      File.delete("#{motif_name}.pwm")  if File.exist?("#{motif_name}.pwm")
+      File.delete("#{motif_name}.pat")  if File.exist?("#{motif_name}.pat")
+    end
+    FileUtils.rm_rf('result_folder')  if Dir.exist?('result_folder')
+    Dir.chdir(@start_dir)
+  end
+  it 'splits plain text into separate files' do
+    run_split_motifs('plain_collection.txt')
+    @motifs_in_collection.each do |motif_name|
+      File.exist?("#{motif_name}.mat").should be_true
+      File.read("#{motif_name}.mat") == File.read("#{motif_name}.mat.result")
+    end
+  end
+  it 'create files with specified extension' do
+    run_split_motifs('plain_collection.txt -e pwm')
+    @motifs_in_collection.each do |motif_name|
+      File.exist?("#{motif_name}.pwm").should be_true
+      File.read("#{motif_name}.pwm") == File.read("#{motif_name}.mat.result")
+    end
+  end
+  
+  context 'when specified folder exist' do
+    before :each do
+      Dir.mkdir('result_folder')  unless Dir.exist?('result_folder')
+    end
+    it 'create files in specified folder' do
+      run_split_motifs('plain_collection.txt -f result_folder')
+      @motifs_in_collection.each do |motif_name|
+        File.exist?(File.join('result_folder', "#{motif_name}.mat")).should be_true
+        File.read(File.join('result_folder', "#{motif_name}.mat")) == File.read("#{motif_name}.mat.result")
+      end
+    end
+  end
+  context 'when specified folder not exist' do
+    before :each do
+      FileUtils.rm_rf('result_folder')  if Dir.exist?('result_folder')
+    end
+    it 'create files in specified folder' do
+      run_split_motifs('plain_collection.txt -f result_folder')
+      @motifs_in_collection.each do |motif_name|
+        File.exist?(File.join('result_folder', "#{motif_name}.mat")).should be_true
+        File.read(File.join('result_folder', "#{motif_name}.mat")) == File.read("#{motif_name}.mat.result")
+      end
+    end
+  end
+  
+  it 'splits motifs from Collections (yamled Bioinform::Collection instances) with appropriate extension' do
+    run_split_motifs('collection.yaml')
+    @motifs_in_collection.each do |motif_name|
+      File.exist?("#{motif_name}.pwm").should be_true
+      File.read("#{motif_name}.pwm") == File.read("#{motif_name}.mat.result")
+    end
+  end
+  it 'splits motifs from Collections with specified extension' do
+    run_split_motifs('collection.yaml -e pat')
+    @motifs_in_collection.each do |motif_name|
+      File.exist?("#{motif_name}.pat").should be_true
+      File.read("#{motif_name}.pat") == File.read("#{motif_name}.mat.result")
+    end
+  end
 end

data/spec/data_models/collection_spec.rb

@@ -1,5 +1,5 @@
-require 'spec_helper'
-require 'bioinform/data_models/collection'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/collection'
 
 module Bioinform
   describe Collection do

data/spec/data_models/pcm_spec.rb

@@ -1,5 +1,5 @@
-require 'spec_helper'
-require 'bioinform/data_models/pcm'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/pcm'
 
 module Bioinform
   describe PCM do

data/spec/data_models/pm_spec.rb

@@ -1,5 +1,5 @@
-require 'spec_helper'
-require 'bioinform/data_models/pm'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/pm'
 
 module Bioinform
   describe PM do
@@ -8,7 +8,7 @@ module Bioinform
         before :each do
           @collection = Collection.new(name: 'Collection 1')
           @matrix = [[1,2,3,4],[5,6,7,8]]
-          @name = 'Motif name'
+          @name = 'PM_motif'
           @background = [0.2,0.3,0.3,0.2]
           @tags = [@collection, 'Collection 2']
           @pm = PM.new(matrix: @matrix, name: @name, background: @background, tags: @tags)
@@ -25,7 +25,7 @@ module Bioinform
         end
       end
     end
-    
+
     describe '#tagged?' do
       context 'when PM marked with Collection object' do
         context 'without collection-name' do
@@ -115,7 +115,7 @@ module Bioinform
       pm_eq = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif')
       pm_neq_matrix = PM.new(matrix: [[1,2,3,4],[15,16,17,18]], name: 'First motif')
       pm_neq_name = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'Second motif')
-      pm_neq_background = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif').background!([1,2,2,1])
+      pm_neq_background = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif').set_parameters(background: [1,2,2,1])
 
       pm.should_not == pm_neq_matrix
       pm.should_not == pm_neq_name
@@ -240,26 +240,9 @@ module Bioinform
       before :each do
         @pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
       end
-      context 'when none arguments passed' do
-        context 'when pm just created' do
-          it 'should be [1,1,1,1]' do
-            @pm.background.should == [1,1,1,1]
-          end
-        end
-        it 'should return background' do
-          @pm.background = [0.2, 0.3, 0.3, 0.2]
-          @pm.background.should == [0.2, 0.3, 0.3, 0.2]
-        end
-      end
-      context 'when one argument passed' do
-        it 'should set background' do
-          @pm.background([0.2,0.3,0.3,0.2])
-          @pm.background.should == [0.2, 0.3, 0.3, 0.2]
-        end
-      end
-      context 'when more than one argument passed' do
-        it 'should raise an ArgumentError' do
-          expect { @pm.background(:first, :second) }.to raise_error ArgumentError
+      context 'when pm just created' do
+        it 'should be [1,1,1,1]' do
+          @pm.background.should == [1,1,1,1]
         end
       end
     end
@@ -335,10 +318,10 @@ module Bioinform
       end
       context 'when background is normalized probabilities' do
         it 'should be 1.0' do
-          @pm_2_positions.background( [0.2, 0.3, 0.3, 0.2] )
+          @pm_2_positions.background = [0.2, 0.3, 0.3, 0.2]
           @pm_2_positions.vocabulary_volume.should == 1.0
 
-          @pm_3_positions.background( [0.2, 0.3, 0.3, 0.2] )
+          @pm_3_positions.background = [0.2, 0.3, 0.3, 0.2]
           @pm_3_positions.vocabulary_volume.should == 1.0
         end
       end

data/spec/data_models/ppm_spec.rb

@@ -1,5 +1,5 @@
-require 'spec_helper'
-require 'bioinform/data_models/pcm'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/pcm'
 
 module Bioinform
   describe PPM do

data/spec/data_models/pwm_spec.rb

@@ -1,5 +1,5 @@
-require 'spec_helper'
-require 'bioinform/data_models/pwm'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/data_models/pwm'
 
 module Bioinform
   describe PWM do
@@ -9,7 +9,7 @@ module Bioinform
         pwm.score_mean.should == 1.5 + 6 + 2
       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]] ).background([0.2, 0.3, 0.3, 0.2])
+        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)
       end
     end

data/spec/fabricators/collection_fabricator.rb

@@ -0,0 +1,8 @@
+Fabricator(:pm_collection, from: Bioinform::Collection, aliases: [:two_elements_collection]) do
+  name 'PM_collection'
+  after_build{|collection| collection << Fabricate(:pm_first) << Fabricate(:pm_second) }
+end
+
+Fabricator(:unnamed_pm_collection, from: :pm_collection) do
+  name nil
+end

data/spec/fabricators/pm_fabricator.rb

@@ -0,0 +1,43 @@
+Fabricator(:pm, from: Bioinform::PM) do
+  initialize_with{ Bioinform::PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'PM_name') }
+end
+
+Fabricator(:pm_unnamed, from: :pm) do
+  name nil
+end
+
+
+Fabricator(:pm_first, from: :pm) do
+  name 'PM_first'
+end
+
+Fabricator(:pm_second, from: :pm) do
+  matrix [[15,16,17,18],[11,21,31,41]]
+  name 'PM_second'
+end
+
+
+Fabricator(:pm_4x4, from: :pm) do
+  matrix [[1,2,3,4],[5,6,7,8],[9,10,11,12],[13,14,15,16]]
+end
+
+Fabricator(:pm_4x4_unnamed, from: :pm_4x4) do
+  name nil
+end
+
+Fabricator(:pm_with_floats, from: :pm_unnamed) do
+  matrix [[1.23, 4.56, 7.8, 9.0], [9, -8.7, 6.54, -3210]]
+end
+
+Fabricator(:pm_1, from: :pm) do
+  matrix [[0,1,2,3],[4,5,6,7]]
+  name 'motif_1'
+end
+Fabricator(:pm_2, from: :pm) do
+  matrix [[1,2,3,4],[5,6,7,8],[9,10,11,12]]
+  name 'motif_2'
+end
+Fabricator(:pm_3, from: :pm) do
+  matrix [[2,3,4,5],[6,7,8,9]]
+  name 'motif_3'
+end