bioinform 0.1.8 → 0.1.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +1 -0
- data/Gemfile +12 -0
- data/Guardfile +9 -0
- data/README.md +7 -1
- data/TODO.txt +8 -0
- data/bioinform.gemspec +7 -5
- data/lib/bioinform.rb +1 -0
- data/lib/bioinform/cli.rb +12 -3
- data/lib/bioinform/cli/convert_motif.rb +108 -0
- data/lib/bioinform/cli/merge_into_collection.rb +6 -2
- data/lib/bioinform/cli/pcm2pwm.rb +1 -1
- data/lib/bioinform/cli/split_motifs.rb +1 -1
- data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +19 -0
- data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +20 -0
- data/lib/bioinform/conversion_algorithms/pcm2pwm_mara_converter.rb +0 -0
- data/lib/bioinform/conversion_algorithms/ppm2pcm_converter.rb +0 -0
- data/lib/bioinform/conversion_algorithms/ppm2pwm_converter.rb +0 -0
- data/lib/bioinform/data_models/collection.rb +21 -35
- data/lib/bioinform/data_models/motif.rb +56 -0
- data/lib/bioinform/data_models/pcm.rb +4 -8
- data/lib/bioinform/data_models/pm.rb +19 -48
- data/lib/bioinform/data_models/pwm.rb +16 -0
- data/lib/bioinform/formatters.rb +2 -0
- data/lib/bioinform/formatters/raw_formatter.rb +41 -0
- data/lib/bioinform/formatters/transfac_formatter.rb +39 -0
- data/lib/bioinform/parsers.rb +2 -1
- data/lib/bioinform/parsers/jaspar_parser.rb +35 -0
- data/lib/bioinform/parsers/string_parser.rb +1 -1
- data/lib/bioinform/parsers/trivial_parser.rb +2 -1
- data/lib/bioinform/parsers/yaml_parser.rb +1 -1
- data/lib/bioinform/support.rb +2 -1
- data/lib/bioinform/support/parameters.rb +27 -18
- data/lib/bioinform/support/strip_doc.rb +9 -0
- data/lib/bioinform/version.rb +1 -1
- data/spec/cli/convert_motif_spec.rb +107 -0
- data/spec/cli/data/merge_into_collection/collection.yaml.result +186 -183
- data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +186 -183
- data/spec/cli/data/split_motifs/collection.yaml +184 -193
- data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +18 -0
- data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +14 -0
- data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +50 -0
- data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +5 -0
- data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +4 -0
- data/spec/data_models/collection_spec.rb +36 -34
- data/spec/data_models/motif_spec.rb +224 -0
- data/spec/data_models/pcm_spec.rb +28 -17
- data/spec/data_models/pm_spec.rb +83 -121
- data/spec/data_models/pwm_spec.rb +38 -0
- data/spec/fabricators/collection_fabricator.rb +2 -2
- data/spec/fabricators/motif_fabricator.rb +33 -0
- data/spec/fabricators/motif_formats_fabricator.rb +125 -0
- data/spec/fabricators/pcm_fabricator.rb +25 -0
- data/spec/fabricators/pm_fabricator.rb +10 -1
- data/spec/fabricators/ppm_fabricator.rb +14 -0
- data/spec/fabricators/pwm_fabricator.rb +16 -0
- data/spec/parsers/trivial_parser_spec.rb +12 -12
- data/spec/parsers/yaml_parser_spec.rb +11 -11
- data/spec/spec_helper.rb +19 -49
- data/spec/spec_helper_source.rb +59 -0
- metadata +78 -7
@@ -1,4 +1,4 @@
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-
Fabricator(:pm,
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+
Fabricator(:pm, class_name: Bioinform::PM) do
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initialize_with{ Bioinform::PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'PM_name') }
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end
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@@ -40,4 +40,13 @@ end
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Fabricator(:pm_3, from: :pm) do
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matrix [[2,3,4,5],[6,7,8,9]]
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name 'motif_3'
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end
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Fabricator(:pm_4,from: :pm) do
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matrix [[1,0,1,0],[0,0,0,0],[1,2,3,4]]
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name 'pm 4'
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end
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Fabricator(:pm_5, from: :pm) do
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matrix [[1,2,1,2],[0,3,6,9],[1,2,3,4]]
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name 'pm 5'
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end
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@@ -0,0 +1,14 @@
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Fabricator(:ppm, class_name: Bioinform::PPM) do
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initialize_with{ Bioinform::PPM.new(matrix: [[0.2, 0.3, 0.3, 0.2],[0.7, 0.2, 0.0, 0.1]]) }
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name 'PPM_name'
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end
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# It has the same name as original pcm because PCM#to_ppm doesn't change the name
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Fabricator(:ppm_by_pcm, class_name: Bioinform::PPM) do
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initialize_with{ Fabricate(:pcm).to_ppm }
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end
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Fabricator(:ppm_pcm_divided_by_count, from: :ppm) do
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# this matrix should be initialized manually - it's used for spec checking PCM#to_ppm
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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]]
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end
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@@ -0,0 +1,16 @@
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Fabricator(:pwm, class_name: Bioinform::PWM) do
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initialize_with{ Bioinform::PWM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'PWM_name')}
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end
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# It has name 'PCM_name' because name isn't converted during #to_pwm
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Fabricator(:pwm_by_pcm, class_name: Bioinform::PWM) do
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initialize_with{ Fabricate(:pcm).to_pwm }
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end
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Fabricator(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_1, from: :pwm) do
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matrix [[-0.47, 0.118, 0.486, -0.47],[0.754, -2.079, -0.47, 0.118]]
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end
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Fabricator(:rounded_upto_3_digits_pwm_by_pcm_with_pseudocount_10, from: :pwm) do
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matrix [[-0.194, 0.057, 0.258, -0.194],[0.425, -0.531, -0.194, 0.057]]
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end
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@@ -4,7 +4,7 @@ require_relative '../../lib/bioinform/data_models/collection'
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module Bioinform
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describe TrivialParser do
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context '
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context '.new' do
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it 'should take the only input argument' do
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TrivialParser.instance_method(:initialize).arity.should == 1
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end
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@@ -20,7 +20,7 @@ module Bioinform
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end
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end
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context '
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context '.split_on_motifs' do
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it 'should be able to get a single PM' do
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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') ]
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end
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@@ -40,24 +40,24 @@ module Bioinform
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end
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describe TrivialCollectionParser do
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end
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let(:collection){ Fabricate(:three_elements_collection) }
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let(:pm_1){ Fabricate(:pm_1) }
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let(:pm_2){ Fabricate(:pm_2) }
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let(:pm_3){ Fabricate(:pm_3) }
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describe '#parse!' do
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it 'can be used to obtain PMs from Collection' do
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@parser = TrivialCollectionParser.new(
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@parser.parse!.should ==
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@parser.parse!.should ==
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@parser = TrivialCollectionParser.new(collection)
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@parser.parse!.should == pm_1
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@parser.parse!.should == pm_2
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@parser.parse!.should == pm_3
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expect{ @parser.parse! }.to raise_error
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end
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end
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describe '
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describe '.split_on_motifs' do
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it 'should be able to split collection into PMs' do
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TrivialCollectionParser.split_on_motifs(
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TrivialCollectionParser.split_on_motifs(collection).should == [pm_1, pm_2, pm_3]
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end
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end
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end
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@@ -27,22 +27,22 @@ module Bioinform
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end
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describe YAMLCollectionParser do
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end
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let(:yamled_collection){ Fabricate(:three_elements_collection).to_yaml }
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let(:pm_1){ Fabricate(:pm_1) }
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let(:pm_2){ Fabricate(:pm_2) }
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let(:pm_3){ Fabricate(:pm_3) }
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context '::split_on_motifs' do
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it 'should be able to split collection into PMs' do
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YAMLCollectionParser.split_on_motifs(
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it 'should be able to split yamled collection into PMs' do
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YAMLCollectionParser.split_on_motifs(yamled_collection).should == [pm_1, pm_2, pm_3]
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end
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end
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context '#parse!' do
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it 'should return PMs which were in encoded YAML format' do
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@parser = YAMLCollectionParser.new(
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@parser.parse!.should ==
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@parser.parse!.should ==
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@parser = YAMLCollectionParser.new(yamled_collection)
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@parser.parse!.should == pm_1
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@parser.parse!.should == pm_2
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@parser.parse!.should == pm_3
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expect{ @parser.parse! }.to raise_error
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end
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end
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data/spec/spec_helper.rb
CHANGED
@@ -1,53 +1,23 @@
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-
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require 'rubygems'
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require 'spork'
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#uncomment the following line to use spork with the debugger
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#require 'spork/ext/ruby-debug'
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Spork.prefork do
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$LOAD_PATH.unshift File.dirname(__FILE__) + '/../lib'
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$LOAD_PATH.unshift File.dirname(__FILE__)
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require 'rspec'
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require 'rspec'
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require 'rspec-given'
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require 'fileutils'
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require 'stringio'
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require 'fabrication'
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require 'fileutils'
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require 'stringio'
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require 'fabrication'
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return {stdout: captured_stdout.string, stderr: captured_stderr.string}
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ensure
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$stdout = orig_stdout
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$stderr = orig_stderr
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end
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# Method stubs $stdin not STDIN !
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def provide_stdin(input, &block)
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orig_stdin = $stdin
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$stdin = StringIO.new(input)
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yield
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ensure
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$stdin = orig_stdin
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end
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def capture_output(&block)
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capture_io(&block)[:stdout]
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end
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def capture_stderr(&block)
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capture_io(&block)[:stderr]
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end
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def parser_specs(parser_klass, good_cases, bad_cases)
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context '#parse!' do
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good_cases.each do |case_description, input_and_result|
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it "should be able to parse #{case_description}" do
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result = parser_klass.new(input_and_result[:input]).parse
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Bioinform::PM.new(result).should == input_and_result[:result]
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end
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end
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bad_cases.each do |case_description, input|
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it "should raise an exception on parsing #{case_description}" do
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expect{ parser_klass.new(input[:input]).parse! }.to raise_error
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end
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end
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end
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require 'fakefs/spec_helpers'
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end
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Spork.each_run do
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require 'spec_helper_source'
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Fabrication.clear_definitions
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end
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@@ -0,0 +1,59 @@
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# from minitest (TODO: make use of minitest, not override it)
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def capture_io(&block)
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orig_stdout, orig_stderr = $stdout, $stderr
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captured_stdout, captured_stderr = StringIO.new, StringIO.new
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$stdout, $stderr = captured_stdout, captured_stderr
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yield
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return {stdout: captured_stdout.string, stderr: captured_stderr.string}
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ensure
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$stdout = orig_stdout
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$stderr = orig_stderr
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end
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# Method stubs $stdin not STDIN !
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def provide_stdin(input, tty = false, &block)
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orig_stdin = $stdin
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$stdin = StringIO.new(input)
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$stdin.send(:define_singleton_method, :tty?){ tty } # Simulate that stdin is tty by default
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yield
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ensure
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$stdin = orig_stdin
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end
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def capture_output(&block)
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capture_io(&block)[:stdout]
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end
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def capture_stderr(&block)
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capture_io(&block)[:stderr]
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end
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def parser_specs(parser_klass, good_cases, bad_cases)
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context '#parse!' do
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good_cases.each do |case_description, input_and_result|
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it "should be able to parse #{case_description}" do
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result = parser_klass.new(input_and_result[:input]).parse
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Bioinform::PM.new(result).should == input_and_result[:result]
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end
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end
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bad_cases.each do |case_description, input|
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it "should raise an exception on parsing #{case_description}" do
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expect{ parser_klass.new(input[:input]).parse! }.to raise_error
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end
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end
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end
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end
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##############################
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def make_file(filename, content)
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File.open(filename, 'w'){|f| f.puts content }
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end
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def motif_filename(motif, model_type)
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"#{motif.name}.#{model_type}"
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end
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def make_model_file(motif, model_type)
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make_file(motif_filename(motif, model_type), motif.send(model_type))
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: bioinform
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.9
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2012-
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date: 2012-12-07 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: activesupport
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@@ -32,7 +32,7 @@ dependencies:
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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-
- -
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- - '='
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- !ruby/object:Gem::Version
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version: 0.5.0
|
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type: :runtime
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@@ -40,9 +40,41 @@ dependencies:
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version_requirements: !ruby/object:Gem::Requirement
|
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none: false
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requirements:
|
43
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-
- -
|
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+
- - '='
|
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- !ruby/object:Gem::Version
|
45
45
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version: 0.5.0
|
46
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- !ruby/object:Gem::Dependency
|
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name: fakefs
|
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requirement: !ruby/object:Gem::Requirement
|
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none: false
|
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requirements:
|
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- - ~>
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description: A bunch of useful classes for bioinformatics
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- prijutme4ty@gmail.com
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|
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|
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|
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|
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|
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- spec/cli/data/merge_into_collection/SP1_f1.pwm
|
@@ -148,20 +194,32 @@ files:
|
|
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|
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|
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|
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|
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|
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|
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- spec/cli/shared_examples/convert_motif/motif_list_empty.rb
|
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|
+
- spec/cli/shared_examples/convert_motif/several_motifs_specified.rb
|
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+
- spec/cli/shared_examples/convert_motif/single_motif_specified.rb
|
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- spec/cli/shared_examples/convert_motif/yield_help_string.rb
|
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- spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
@@ -200,6 +258,7 @@ summary: Classes for work with different input formats of positional matrices an
|
|
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|
symbols
|
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|
test_files:
|
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|
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|
261
|
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|
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|
- spec/cli/data/merge_into_collection/GABPA_f1.pwm
|
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|
- spec/cli/data/merge_into_collection/KLF4_f2.pwm
|
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|
- spec/cli/data/merge_into_collection/SP1_f1.pwm
|
@@ -221,20 +280,32 @@ test_files:
|
|
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280
|
- spec/cli/data/split_motifs/plain_collection.txt
|
222
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|
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|
223
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|
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|
283
|
+
- spec/cli/shared_examples/convert_motif/motif_list_empty.rb
|
284
|
+
- spec/cli/shared_examples/convert_motif/several_motifs_specified.rb
|
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|
+
- spec/cli/shared_examples/convert_motif/single_motif_specified.rb
|
286
|
+
- spec/cli/shared_examples/convert_motif/yield_help_string.rb
|
287
|
+
- spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb
|
224
288
|
- spec/cli/split_motifs_spec.rb
|
225
289
|
- spec/data_models/collection_spec.rb
|
290
|
+
- spec/data_models/motif_spec.rb
|
226
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|
- spec/data_models/pcm_spec.rb
|
227
292
|
- spec/data_models/pm_spec.rb
|
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|
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|
229
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|
- spec/data_models/pwm_spec.rb
|
230
295
|
- spec/fabricators/collection_fabricator.rb
|
296
|
+
- spec/fabricators/motif_fabricator.rb
|
297
|
+
- spec/fabricators/motif_formats_fabricator.rb
|
298
|
+
- spec/fabricators/pcm_fabricator.rb
|
231
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|
- spec/fabricators/pm_fabricator.rb
|
300
|
+
- spec/fabricators/ppm_fabricator.rb
|
301
|
+
- spec/fabricators/pwm_fabricator.rb
|
232
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|
- spec/parsers/parser_spec.rb
|
233
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|
- spec/parsers/string_fantom_parser_spec.rb
|
234
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|
- spec/parsers/string_parser_spec.rb
|
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|
- spec/parsers/trivial_parser_spec.rb
|
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|
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|
237
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|
- spec/spec_helper.rb
|
308
|
+
- spec/spec_helper_source.rb
|
238
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|
- spec/support/advanced_scan_spec.rb
|
239
310
|
- spec/support/array_product_spec.rb
|
240
311
|
- spec/support/array_zip_spec.rb
|