bioinform 0.1.8 → 0.1.9

data/spec/fabricators/pm_fabricator.rb

@@ -1,4 +1,4 @@
-Fabricator(:pm, from: Bioinform::PM) do
+Fabricator(:pm, class_name: Bioinform::PM) do
   initialize_with{ Bioinform::PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'PM_name') }
 end
 
@@ -40,4 +40,13 @@ end
 Fabricator(:pm_3, from: :pm) do
   matrix [[2,3,4,5],[6,7,8,9]]
   name 'motif_3'
+end
+
+Fabricator(:pm_4,from: :pm) do
+  matrix [[1,0,1,0],[0,0,0,0],[1,2,3,4]]
+  name 'pm 4'
+end
+Fabricator(:pm_5, from: :pm) do
+  matrix [[1,2,1,2],[0,3,6,9],[1,2,3,4]]
+  name 'pm 5'
 end

data/spec/fabricators/ppm_fabricator.rb

@@ -0,0 +1,14 @@
+Fabricator(:ppm, class_name: Bioinform::PPM) do
+  initialize_with{ Bioinform::PPM.new(matrix: [[0.2, 0.3, 0.3, 0.2],[0.7, 0.2, 0.0, 0.1]]) }
+  name 'PPM_name'
+end
+
+# It has the same name as original pcm because PCM#to_ppm doesn't change the name
+Fabricator(:ppm_by_pcm, class_name: Bioinform::PPM) do
+  initialize_with{ Fabricate(:pcm).to_ppm }
+end
+
+Fabricator(:ppm_pcm_divided_by_count, from: :ppm) do
+# this matrix should be initialized manually - it's used for spec checking PCM#to_ppm
+  matrix [[1.0/7.0, 2.0/7.0, 3.0/7.0, 1.0/7.0], [4.0/7.0, 0.0/7.0, 1.0/7.0, 2.0/7.0]]
+end

data/spec/fabricators/pwm_fabricator.rb

@@ -0,0 +1,16 @@
+Fabricator(:pwm, class_name: Bioinform::PWM) do
+  initialize_with{ Bioinform::PWM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'PWM_name')}
+end
+
+# It has name 'PCM_name' because name isn't converted during #to_pwm
+Fabricator(:pwm_by_pcm, class_name: Bioinform::PWM) do
+  initialize_with{ Fabricate(:pcm).to_pwm }
+end
+
+Fabricator(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_1, from: :pwm) do
+  matrix [[-0.47, 0.118, 0.486, -0.47],[0.754, -2.079, -0.47, 0.118]]
+end
+
+Fabricator(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_10, from: :pwm) do
+  matrix [[-0.194, 0.057, 0.258, -0.194],[0.425, -0.531, -0.194, 0.057]]
+end

data/spec/parsers/trivial_parser_spec.rb

@@ -4,7 +4,7 @@ require_relative '../../lib/bioinform/data_models/collection'
 
 module Bioinform
   describe TrivialParser do
-    context '#initialize' do
+    context '.new' do
       it 'should take the only input argument' do
         TrivialParser.instance_method(:initialize).arity.should == 1
       end
@@ -20,7 +20,7 @@ module Bioinform
       end
     end
 
-    context '::split_on_motifs' do
+    context '.split_on_motifs' do
       it 'should be able to get a single PM' do
         TrivialParser.split_on_motifs({matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name'}, PM).should == [ PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name:'Name') ]
       end
@@ -40,24 +40,24 @@ module Bioinform
   end
 
   describe TrivialCollectionParser do
-    before :each do
-      @pm_1 = Fabricate(:pm_first)
-      @pm_2 = Fabricate(:pm_second)
-      @collection = Fabricate(:two_elements_collection)
-    end
+    let(:collection){ Fabricate(:three_elements_collection) }
+    let(:pm_1){ Fabricate(:pm_1) }
+    let(:pm_2){ Fabricate(:pm_2) }
+    let(:pm_3){ Fabricate(:pm_3) }
 
     describe '#parse!' do
       it 'can be used to obtain PMs from Collection' do
-        @parser = TrivialCollectionParser.new(@collection)
-        @parser.parse!.should == @pm_1
-        @parser.parse!.should == @pm_2
+        @parser = TrivialCollectionParser.new(collection)
+        @parser.parse!.should == pm_1
+        @parser.parse!.should == pm_2
+        @parser.parse!.should == pm_3
         expect{ @parser.parse! }.to raise_error
       end
     end
 
-    describe '::split_on_motifs' do
+    describe '.split_on_motifs' do
       it 'should be able to split collection into PMs' do
-        TrivialCollectionParser.split_on_motifs(@collection).should == [@pm_1, @pm_2]
+        TrivialCollectionParser.split_on_motifs(collection).should == [pm_1, pm_2, pm_3]
       end
     end
   end

data/spec/parsers/yaml_parser_spec.rb

@@ -27,22 +27,22 @@ module Bioinform
   end
 
   describe YAMLCollectionParser do
-    before :each do
-      @pm_1 = Fabricate(:pm_first)
-      @pm_2 = Fabricate(:pm_second)
-      @collection = Collection.new
-      @collection << @pm_1 << @pm_2
-    end
+    let(:yamled_collection){ Fabricate(:three_elements_collection).to_yaml }
+    let(:pm_1){ Fabricate(:pm_1) }
+    let(:pm_2){ Fabricate(:pm_2) }
+    let(:pm_3){ Fabricate(:pm_3) }
+
     context '::split_on_motifs' do
-      it 'should be able to split collection into PMs' do
-        YAMLCollectionParser.split_on_motifs(@collection.to_yaml).should == [@pm_1, @pm_2]
+      it 'should be able to split yamled collection into PMs' do
+        YAMLCollectionParser.split_on_motifs(yamled_collection).should == [pm_1, pm_2, pm_3]
       end
     end
     context '#parse!' do
       it 'should return PMs which were in encoded YAML format' do
-        @parser = YAMLCollectionParser.new(@collection.to_yaml)
-        @parser.parse!.should == @pm_1
-        @parser.parse!.should == @pm_2
+        @parser = YAMLCollectionParser.new(yamled_collection)
+        @parser.parse!.should == pm_1
+        @parser.parse!.should == pm_2
+        @parser.parse!.should == pm_3
         expect{ @parser.parse! }.to raise_error
       end
     end

data/spec/spec_helper.rb

@@ -1,53 +1,23 @@
-$LOAD_PATH.unshift File.dirname(__FILE__) + '/../lib'
-$LOAD_PATH.unshift File.dirname(__FILE__)
+require 'rubygems'
+require 'spork'
+#uncomment the following line to use spork with the debugger
+#require 'spork/ext/ruby-debug'
+
+Spork.prefork do
+  $LOAD_PATH.unshift File.dirname(__FILE__) + '/../lib'
+  $LOAD_PATH.unshift File.dirname(__FILE__)
 
-require 'rspec'
+  require 'rspec'
+  require 'rspec-given'
 
-require 'fileutils'
-require 'stringio'
-require 'fabrication'
+  require 'fileutils'
+  require 'stringio'
+  require 'fabrication'
 
-# from minitest
-def capture_io(&block)
-  orig_stdout, orig_stderr = $stdout, $stderr
-  captured_stdout, captured_stderr = StringIO.new, StringIO.new
-  $stdout, $stderr = captured_stdout, captured_stderr
-  yield
-  return {stdout: captured_stdout.string, stderr: captured_stderr.string}
-ensure
-  $stdout = orig_stdout
-  $stderr = orig_stderr
-end
-
-# Method stubs $stdin not STDIN !
-def provide_stdin(input, &block)
-  orig_stdin = $stdin
-  $stdin = StringIO.new(input)
-  yield
-ensure
-  $stdin = orig_stdin
-end
-
-def capture_output(&block)
-  capture_io(&block)[:stdout]
-end
-def capture_stderr(&block)
-  capture_io(&block)[:stderr]
-end
-
-def parser_specs(parser_klass, good_cases, bad_cases)
-  context '#parse!' do
-    good_cases.each do |case_description, input_and_result|
-      it "should be able to parse #{case_description}" do
-        result = parser_klass.new(input_and_result[:input]).parse
-        Bioinform::PM.new(result).should == input_and_result[:result]
-      end
-    end
-
-    bad_cases.each do |case_description, input|
-      it "should raise an exception on parsing #{case_description}" do
-        expect{ parser_klass.new(input[:input]).parse! }.to raise_error
-      end
-    end
-  end
+  require 'fakefs/spec_helpers'  
+end
+
+Spork.each_run do
+  require 'spec_helper_source'
+  Fabrication.clear_definitions
 end

data/spec/spec_helper_source.rb

@@ -0,0 +1,59 @@
+# from minitest (TODO: make use of minitest, not override it)
+def capture_io(&block)
+  orig_stdout, orig_stderr = $stdout, $stderr
+  captured_stdout, captured_stderr = StringIO.new, StringIO.new
+  $stdout, $stderr = captured_stdout, captured_stderr
+  yield
+  return {stdout: captured_stdout.string, stderr: captured_stderr.string}
+ensure
+  $stdout = orig_stdout
+  $stderr = orig_stderr
+end
+
+# Method stubs $stdin not STDIN !
+def provide_stdin(input, tty = false, &block)
+  orig_stdin = $stdin
+  $stdin = StringIO.new(input)
+  $stdin.send(:define_singleton_method, :tty?){ tty }  # Simulate that stdin is tty by default
+  yield
+ensure
+  $stdin = orig_stdin
+end
+
+def capture_output(&block)
+  capture_io(&block)[:stdout]
+end
+def capture_stderr(&block)
+  capture_io(&block)[:stderr]
+end
+
+def parser_specs(parser_klass, good_cases, bad_cases)
+  context '#parse!' do
+    good_cases.each do |case_description, input_and_result|
+      it "should be able to parse #{case_description}" do
+        result = parser_klass.new(input_and_result[:input]).parse
+        Bioinform::PM.new(result).should == input_and_result[:result]
+      end
+    end
+
+    bad_cases.each do |case_description, input|
+      it "should raise an exception on parsing #{case_description}" do
+        expect{ parser_klass.new(input[:input]).parse! }.to raise_error
+      end
+    end
+  end
+end
+
+##############################
+
+def make_file(filename, content)
+  File.open(filename, 'w'){|f| f.puts content }
+end
+
+def motif_filename(motif, model_type)
+  "#{motif.name}.#{model_type}"
+end
+
+def make_model_file(motif, model_type)
+  make_file(motif_filename(motif, model_type), motif.send(model_type))
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.8
+  version: 0.1.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-15 00:00:00.000000000 Z
+date: 2012-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -32,7 +32,7 @@ dependencies:
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
         version: 0.5.0
   type: :runtime
@@ -40,9 +40,41 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
         version: 0.5.0
+- !ruby/object:Gem::Dependency
+  name: fakefs
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.2
+- !ruby/object:Gem::Dependency
+  name: fabrication
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.5.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.5.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -60,13 +92,13 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: fabrication
+  name: rspec-given
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 2.2.3
+        version: 2.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -74,7 +106,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 2.2.3
+        version: 2.0.0
 description: A bunch of useful classes for bioinformatics
 email:
 - prijutme4ty@gmail.com
@@ -87,6 +119,7 @@ extra_rdoc_files: []
 files:
 - .gitignore
 - Gemfile
+- Guardfile
 - LICENSE
 - README.md
 - Rakefile
@@ -97,16 +130,27 @@ files:
 - bioinform.gemspec
 - lib/bioinform.rb
 - lib/bioinform/cli.rb
+- lib/bioinform/cli/convert_motif.rb
 - lib/bioinform/cli/merge_into_collection.rb
 - lib/bioinform/cli/pcm2pwm.rb
 - lib/bioinform/cli/split_motifs.rb
+- lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb
+- lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb
+- lib/bioinform/conversion_algorithms/pcm2pwm_mara_converter.rb
+- lib/bioinform/conversion_algorithms/ppm2pcm_converter.rb
+- lib/bioinform/conversion_algorithms/ppm2pwm_converter.rb
 - lib/bioinform/data_models.rb
 - lib/bioinform/data_models/collection.rb
+- lib/bioinform/data_models/motif.rb
 - lib/bioinform/data_models/pcm.rb
 - lib/bioinform/data_models/pm.rb
 - lib/bioinform/data_models/ppm.rb
 - lib/bioinform/data_models/pwm.rb
+- lib/bioinform/formatters.rb
+- lib/bioinform/formatters/raw_formatter.rb
+- lib/bioinform/formatters/transfac_formatter.rb
 - lib/bioinform/parsers.rb
+- lib/bioinform/parsers/jaspar_parser.rb
 - lib/bioinform/parsers/parser.rb
 - lib/bioinform/parsers/splittable_parser.rb
 - lib/bioinform/parsers/string_fantom_parser.rb
@@ -125,8 +169,10 @@ files:
 - lib/bioinform/support/parameters.rb
 - lib/bioinform/support/partial_sums.rb
 - lib/bioinform/support/same_by.rb
+- lib/bioinform/support/strip_doc.rb
 - lib/bioinform/version.rb
 - spec/cli/cli_spec.rb
+- spec/cli/convert_motif_spec.rb
 - spec/cli/data/merge_into_collection/GABPA_f1.pwm
 - spec/cli/data/merge_into_collection/KLF4_f2.pwm
 - spec/cli/data/merge_into_collection/SP1_f1.pwm
@@ -148,20 +194,32 @@ files:
 - spec/cli/data/split_motifs/plain_collection.txt
 - spec/cli/merge_into_collection_spec.rb
 - spec/cli/pcm2pwm_spec.rb
+- spec/cli/shared_examples/convert_motif/motif_list_empty.rb
+- spec/cli/shared_examples/convert_motif/several_motifs_specified.rb
+- spec/cli/shared_examples/convert_motif/single_motif_specified.rb
+- spec/cli/shared_examples/convert_motif/yield_help_string.rb
+- spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb
 - spec/cli/split_motifs_spec.rb
 - spec/data_models/collection_spec.rb
+- spec/data_models/motif_spec.rb
 - spec/data_models/pcm_spec.rb
 - spec/data_models/pm_spec.rb
 - spec/data_models/ppm_spec.rb
 - spec/data_models/pwm_spec.rb
 - spec/fabricators/collection_fabricator.rb
+- spec/fabricators/motif_fabricator.rb
+- spec/fabricators/motif_formats_fabricator.rb
+- spec/fabricators/pcm_fabricator.rb
 - spec/fabricators/pm_fabricator.rb
+- spec/fabricators/ppm_fabricator.rb
+- spec/fabricators/pwm_fabricator.rb
 - spec/parsers/parser_spec.rb
 - spec/parsers/string_fantom_parser_spec.rb
 - spec/parsers/string_parser_spec.rb
 - spec/parsers/trivial_parser_spec.rb
 - spec/parsers/yaml_parser_spec.rb
 - spec/spec_helper.rb
+- spec/spec_helper_source.rb
 - spec/support/advanced_scan_spec.rb
 - spec/support/array_product_spec.rb
 - spec/support/array_zip_spec.rb
@@ -200,6 +258,7 @@ summary: Classes for work with different input formats of positional matrices an
   symbols
 test_files:
 - spec/cli/cli_spec.rb
+- spec/cli/convert_motif_spec.rb
 - spec/cli/data/merge_into_collection/GABPA_f1.pwm
 - spec/cli/data/merge_into_collection/KLF4_f2.pwm
 - spec/cli/data/merge_into_collection/SP1_f1.pwm
@@ -221,20 +280,32 @@ test_files:
 - spec/cli/data/split_motifs/plain_collection.txt
 - spec/cli/merge_into_collection_spec.rb
 - spec/cli/pcm2pwm_spec.rb
+- spec/cli/shared_examples/convert_motif/motif_list_empty.rb
+- spec/cli/shared_examples/convert_motif/several_motifs_specified.rb
+- spec/cli/shared_examples/convert_motif/single_motif_specified.rb
+- spec/cli/shared_examples/convert_motif/yield_help_string.rb
+- spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb
 - spec/cli/split_motifs_spec.rb
 - spec/data_models/collection_spec.rb
+- spec/data_models/motif_spec.rb
 - spec/data_models/pcm_spec.rb
 - spec/data_models/pm_spec.rb
 - spec/data_models/ppm_spec.rb
 - spec/data_models/pwm_spec.rb
 - spec/fabricators/collection_fabricator.rb
+- spec/fabricators/motif_fabricator.rb
+- spec/fabricators/motif_formats_fabricator.rb
+- spec/fabricators/pcm_fabricator.rb
 - spec/fabricators/pm_fabricator.rb
+- spec/fabricators/ppm_fabricator.rb
+- spec/fabricators/pwm_fabricator.rb
 - spec/parsers/parser_spec.rb
 - spec/parsers/string_fantom_parser_spec.rb
 - spec/parsers/string_parser_spec.rb
 - spec/parsers/trivial_parser_spec.rb
 - spec/parsers/yaml_parser_spec.rb
 - spec/spec_helper.rb
+- spec/spec_helper_source.rb
 - spec/support/advanced_scan_spec.rb
 - spec/support/array_product_spec.rb
 - spec/support/array_zip_spec.rb