bioinform 0.1.12 → 0.1.13

data/spec/cli/merge_into_collection_spec.rb

@@ -1,100 +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
+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

@@ -1,80 +1,80 @@
-require 'shellwords'
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/cli/pcm2pwm'
-
-
-def run_pcm2pwm(cmd)
-  Bioinform::CLI::PCM2PWM.main(cmd.shellsplit)
-end
-
-describe Bioinform::CLI::PCM2PWM do
-  before :each do
-    @start_dir = Dir.pwd
-    Dir.chdir File.join(File.dirname(__FILE__), 'data', 'pcm2pwm')
-  end
-  after :each do
-    File.delete('KLF4_f2.pwm')  if File.exist?('KLF4_f2.pwm')
-    File.delete('SP1_f1.pwm')  if File.exist?('SP1_f1.pwm')
-    File.delete('KLF4_f2.pat')  if File.exist?('KLF4_f2.pat')
-    File.delete('KLF4 f2 spaced name.pwm')  if File.exist?('KLF4 f2 spaced name.pwm')
-    FileUtils.rm_rf('pwm_folder')  if Dir.exist?('pwm_folder')
-    Dir.chdir(@start_dir)
-  end
-
-  it 'should transform single PCM to PWM' do
-    run_pcm2pwm('KLF4_f2.pcm')
-    File.exist?('KLF4_f2.pwm').should be_true
-    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
-  end
-
-  it 'should transform multiple PCMs to PWMs' do
-    run_pcm2pwm('KLF4_f2.pcm SP1_f1.pcm')
-
-    File.exist?('KLF4_f2.pwm').should be_true
-    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
-
-    File.exist?('SP1_f1.pwm').should be_true
-    File.read('SP1_f1.pwm').should == File.read('SP1_f1.pwm.result')
-  end
-
-  it 'should transform extension to specified with --extension option' do
-    run_pcm2pwm('KLF4_f2.pcm --extension=pat')
-    File.exist?('KLF4_f2.pat').should be_true
-    File.read('KLF4_f2.pat').should == File.read('KLF4_f2.pwm.result')
-  end
-
-  it 'should save PWMs into folder specified with --folder option when folder exists' do
-    Dir.mkdir('pwm_folder')  unless Dir.exist?('pwm_folder')
-    run_pcm2pwm('KLF4_f2.pcm --folder=pwm_folder')
-    File.exist?('pwm_folder/KLF4_f2.pwm').should be_true
-    File.read('pwm_folder/KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
-  end
-  it 'should save PWMs into folder specified with --folder option' do
-    FileUtils.rm_rf('pwm_folder')  if Dir.exist?('pwm_folder')
-    run_pcm2pwm('KLF4_f2.pcm --folder=pwm_folder')
-    File.exist?('pwm_folder/KLF4_f2.pwm').should be_true
-    File.read('pwm_folder/KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
-  end
-
-  it 'should process PCMs with names obtained from STDIN' do
-    provide_stdin('KLF4_f2.pcm SP1_f1.pcm') { run_pcm2pwm('') }
-    File.exist?('KLF4_f2.pwm').should be_true
-    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
-
-    File.exist?('SP1_f1.pwm').should be_true
-    File.read('SP1_f1.pwm').should == File.read('SP1_f1.pwm.result')
-  end
-
-  it 'should process PCMs with names obtained from STDIN when there are some options' do
-    provide_stdin('KLF4_f2.pcm') { run_pcm2pwm('-e pat') }
-    File.exist?('KLF4_f2.pat').should be_true
-    File.read('KLF4_f2.pat').should == File.read('KLF4_f2.pwm.result')
-  end
-
-  it 'should process PCMs having filename with spaces' do
-    run_pcm2pwm('"KLF4 f2 spaced name.pcm"')
-    File.exist?('KLF4 f2 spaced name.pwm').should be_true
-    File.read('KLF4 f2 spaced name.pwm').should == File.read('KLF4_f2.pwm.result')
-  end
-
+require 'shellwords'
+require_relative '../spec_helper'
+require_relative '../../lib/bioinform/cli/pcm2pwm'
+
+
+def run_pcm2pwm(cmd)
+  Bioinform::CLI::PCM2PWM.main(cmd.shellsplit)
+end
+
+describe Bioinform::CLI::PCM2PWM do
+  before :each do
+    @start_dir = Dir.pwd
+    Dir.chdir File.join(File.dirname(__FILE__), 'data', 'pcm2pwm')
+  end
+  after :each do
+    File.delete('KLF4_f2.pwm')  if File.exist?('KLF4_f2.pwm')
+    File.delete('SP1_f1.pwm')  if File.exist?('SP1_f1.pwm')
+    File.delete('KLF4_f2.pat')  if File.exist?('KLF4_f2.pat')
+    File.delete('KLF4 f2 spaced name.pwm')  if File.exist?('KLF4 f2 spaced name.pwm')
+    FileUtils.rm_rf('pwm_folder')  if Dir.exist?('pwm_folder')
+    Dir.chdir(@start_dir)
+  end
+
+  it 'should transform single PCM to PWM' do
+    run_pcm2pwm('KLF4_f2.pcm')
+    File.exist?('KLF4_f2.pwm').should be_true
+    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
+  end
+
+  it 'should transform multiple PCMs to PWMs' do
+    run_pcm2pwm('KLF4_f2.pcm SP1_f1.pcm')
+
+    File.exist?('KLF4_f2.pwm').should be_true
+    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
+
+    File.exist?('SP1_f1.pwm').should be_true
+    File.read('SP1_f1.pwm').should == File.read('SP1_f1.pwm.result')
+  end
+
+  it 'should transform extension to specified with --extension option' do
+    run_pcm2pwm('KLF4_f2.pcm --extension=pat')
+    File.exist?('KLF4_f2.pat').should be_true
+    File.read('KLF4_f2.pat').should == File.read('KLF4_f2.pwm.result')
+  end
+
+  it 'should save PWMs into folder specified with --folder option when folder exists' do
+    Dir.mkdir('pwm_folder')  unless Dir.exist?('pwm_folder')
+    run_pcm2pwm('KLF4_f2.pcm --folder=pwm_folder')
+    File.exist?('pwm_folder/KLF4_f2.pwm').should be_true
+    File.read('pwm_folder/KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
+  end
+  it 'should save PWMs into folder specified with --folder option' do
+    FileUtils.rm_rf('pwm_folder')  if Dir.exist?('pwm_folder')
+    run_pcm2pwm('KLF4_f2.pcm --folder=pwm_folder')
+    File.exist?('pwm_folder/KLF4_f2.pwm').should be_true
+    File.read('pwm_folder/KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
+  end
+
+  it 'should process PCMs with names obtained from STDIN' do
+    provide_stdin('KLF4_f2.pcm SP1_f1.pcm') { run_pcm2pwm('') }
+    File.exist?('KLF4_f2.pwm').should be_true
+    File.read('KLF4_f2.pwm').should == File.read('KLF4_f2.pwm.result')
+
+    File.exist?('SP1_f1.pwm').should be_true
+    File.read('SP1_f1.pwm').should == File.read('SP1_f1.pwm.result')
+  end
+
+  it 'should process PCMs with names obtained from STDIN when there are some options' do
+    provide_stdin('KLF4_f2.pcm') { run_pcm2pwm('-e pat') }
+    File.exist?('KLF4_f2.pat').should be_true
+    File.read('KLF4_f2.pat').should == File.read('KLF4_f2.pwm.result')
+  end
+
+  it 'should process PCMs having filename with spaces' do
+    run_pcm2pwm('"KLF4 f2 spaced name.pcm"')
+    File.exist?('KLF4 f2 spaced name.pwm').should be_true
+    File.read('KLF4 f2 spaced name.pwm').should == File.read('KLF4_f2.pwm.result')
+  end
+
 end

data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb

@@ -1,18 +1,18 @@
-require_relative '../../../spec_helper'
-require_relative 'yield_help_string'
-
-shared_examples 'motif list is empty' do
-  context  'motif list is empty' do
-    Given(:motif_list) { [] }
-    
-    context 'with options' do
-      Given(:options) { '--formatter default  --silent' }
-      include_examples 'yield help string'
-    end
-    
-    context 'without options' do
-      Given(:options){ '' }
-      include_examples 'yield help string'
-    end
-  end
+require_relative '../../../spec_helper'
+require_relative 'yield_help_string'
+
+shared_examples 'motif list is empty' do
+  context  'motif list is empty' do
+    Given(:motif_list) { [] }
+    
+    context 'with options' do
+      Given(:options) { '--formatter default  --silent' }
+      include_examples 'yield help string'
+    end
+    
+    context 'without options' do
+      Given(:options){ '' }
+      include_examples 'yield help string'
+    end
+  end
 end

data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb

@@ -1,14 +1,14 @@
-require_relative '../../../spec_helper'
-
-shared_examples 'several motifs specified' do
-  context 'several motifs specified' do
-    Given {
-      make_model_file(sp1_f1, 'pcm')
-      make_model_file(klf4_f2, 'pcm')
-    }
-    Given(:motif_list) { [sp1_f1, klf4_f2] }  
-    Given(:model_from) { 'pcm' }
-    Given(:model_to) { 'pwm' }
-    Then { resulting_stdout.should == [sp1_f1.pwm, klf4_f2.pwm].join("\n") }
-  end
-end
+require_relative '../../../spec_helper'
+
+shared_examples 'several motifs specified' do
+  context 'several motifs specified' do
+    Given {
+      make_model_file(sp1_f1, 'pcm')
+      make_model_file(klf4_f2, 'pcm')
+    }
+    Given(:motif_list) { [sp1_f1, klf4_f2] }  
+    Given(:model_from) { 'pcm' }
+    Given(:model_to) { 'pwm' }
+    Then { resulting_stdout.should == [sp1_f1.pwm, klf4_f2.pwm].join("\n") }
+  end
+end

data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb

@@ -1,50 +1,50 @@
-require_relative '../../../spec_helper'
-
-shared_examples 'single motif specified' do
-  context 'single motif specified' do
-    Given {
-      make_model_file(sp1_f1, model_from)
-    }
-    Given(:motif_list) { [sp1_f1] }
-
-    context 'when input is a pcm' do
-      Given(:model_from) { 'pcm' }
-
-      context 'pwm conversion invoked' do
-        Given(:model_to) { 'pwm' }
-        Then { resulting_stdout.should == sp1_f1.pwm }
-      end
-
-      context 'ppm conversion invoked' do
-        Given(:model_to) { 'ppm' }
-        Then { resulting_stdout.should == sp1_f1.ppm }
-      end
-    end
-    
-    context 'when input is a pwm' do
-      Given(:model_from) { 'pwm' }
-
-      context 'pcm conversion invoked' do
-        Given(:model_to) { 'pcm' }
-        include_examples 'yields motif conversion error'
-      end
-
-      context 'ppm conversion invoked' do
-        Given(:model_to) { 'ppm' }
-        include_examples 'yields motif conversion error'
-      end
-    end
-
-    context 'if there exist other files in current folder' do
-      Given {
-        make_model_file(sp1_f1, model_from)
-        make_model_file(klf4_f2, model_from)
-      }
-      Given(:model_from) { 'pcm' }
-      Given(:model_to) { 'pwm' }
-      Then { resulting_stdout.should == sp1_f1.pwm }
-      Then { resulting_stdout.should_not match(klf4_f2.pwm) }
-    end
-    
-  end
+require_relative '../../../spec_helper'
+
+shared_examples 'single motif specified' do
+  context 'single motif specified' do
+    Given {
+      make_model_file(sp1_f1, model_from)
+    }
+    Given(:motif_list) { [sp1_f1] }
+
+    context 'when input is a pcm' do
+      Given(:model_from) { 'pcm' }
+
+      context 'pwm conversion invoked' do
+        Given(:model_to) { 'pwm' }
+        Then { resulting_stdout.should == sp1_f1.pwm }
+      end
+
+      context 'ppm conversion invoked' do
+        Given(:model_to) { 'ppm' }
+        Then { resulting_stdout.should == sp1_f1.ppm }
+      end
+    end
+    
+    context 'when input is a pwm' do
+      Given(:model_from) { 'pwm' }
+
+      context 'pcm conversion invoked' do
+        Given(:model_to) { 'pcm' }
+        include_examples 'yields motif conversion error'
+      end
+
+      context 'ppm conversion invoked' do
+        Given(:model_to) { 'ppm' }
+        include_examples 'yields motif conversion error'
+      end
+    end
+
+    context 'if there exist other files in current folder' do
+      Given {
+        make_model_file(sp1_f1, model_from)
+        make_model_file(klf4_f2, model_from)
+      }
+      Given(:model_from) { 'pcm' }
+      Given(:model_to) { 'pwm' }
+      Then { resulting_stdout.should == sp1_f1.pwm }
+      Then { resulting_stdout.should_not match(klf4_f2.pwm) }
+    end
+    
+  end
 end

data/spec/cli/shared_examples/convert_motif/yield_help_string.rb

@@ -1,5 +1,5 @@
-require_relative '../../../spec_helper'
-
-shared_examples 'yield help string' do
-  Then { resulting_stdout.should match(/Usage:.*Options:/m) }
+require_relative '../../../spec_helper'
+
+shared_examples 'yield help string' do
+  Then { resulting_stdout.should match(/Usage:.*Options:/m) }
 end

data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb

@@ -1,4 +1,4 @@
-shared_examples 'yields motif conversion error' do
-  Then { resulting_stderr.should match "One can't convert from #{model_from} data-model to #{model_to} data-model" }
-  Then { resulting_stderr.should match "Error! Conversion wasn't performed" }
+shared_examples 'yields motif conversion error' do
+  Then { resulting_stderr.should match "One can't convert from #{model_from} data-model to #{model_to} data-model" }
+  Then { resulting_stderr.should match "Error! Conversion wasn't performed" }
 end