bioinform 0.1.12 → 0.1.13

data/spec/cli/split_motifs_spec.rb

@@ -1,77 +1,77 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/cli/split_motifs'
-
-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
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/cli/split_motifs'
+
+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

@@ -1,98 +1,98 @@
-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
+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