bioinform 0.1.12 → 0.1.13
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- checksums.yaml +4 -4
- data/.gitignore +17 -17
- data/Gemfile +16 -16
- data/LICENSE +21 -21
- data/README.md +35 -35
- data/Rakefile +4 -4
- data/TODO.txt +37 -37
- data/bin/merge_into_collection +3 -3
- data/bin/pcm2pwm +3 -3
- data/bin/split_motifs +3 -3
- data/bioinform.gemspec +19 -19
- data/lib/bioinform/cli/convert_motif.rb +107 -107
- data/lib/bioinform/cli/merge_into_collection.rb +79 -79
- data/lib/bioinform/cli/pcm2pwm.rb +46 -46
- data/lib/bioinform/cli/split_motifs.rb +46 -46
- data/lib/bioinform/cli.rb +29 -29
- data/lib/bioinform/conversion_algorithms/pcm2ppm_converter.rb +18 -18
- data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb +19 -19
- data/lib/bioinform/data_models/collection.rb +74 -74
- data/lib/bioinform/data_models/motif.rb +55 -55
- data/lib/bioinform/data_models/pcm.rb +23 -23
- data/lib/bioinform/data_models/pm.rb +169 -169
- data/lib/bioinform/data_models/ppm.rb +9 -9
- data/lib/bioinform/data_models/pwm.rb +55 -55
- data/lib/bioinform/data_models.rb +10 -10
- data/lib/bioinform/formatters/raw_formatter.rb +40 -40
- data/lib/bioinform/formatters/transfac_formatter.rb +38 -38
- data/lib/bioinform/formatters.rb +1 -1
- data/lib/bioinform/parsers/jaspar_parser.rb +34 -34
- data/lib/bioinform/parsers/parser.rb +87 -87
- data/lib/bioinform/parsers/splittable_parser.rb +56 -56
- data/lib/bioinform/parsers/string_fantom_parser.rb +34 -34
- data/lib/bioinform/parsers/string_parser.rb +71 -71
- data/lib/bioinform/parsers/trivial_parser.rb +33 -33
- data/lib/bioinform/parsers/yaml_parser.rb +34 -34
- data/lib/bioinform/parsers.rb +6 -6
- data/lib/bioinform/support/array_product.rb +5 -5
- data/lib/bioinform/support/array_zip.rb +5 -5
- data/lib/bioinform/support/collect_hash.rb +6 -6
- data/lib/bioinform/support/deep_dup.rb +4 -4
- data/lib/bioinform/support/delete_many.rb +13 -13
- data/lib/bioinform/support/inverf.rb +12 -12
- data/lib/bioinform/support/multiline_squish.rb +5 -5
- data/lib/bioinform/support/parameters.rb +27 -27
- data/lib/bioinform/support/partial_sums.rb +15 -15
- data/lib/bioinform/support/same_by.rb +12 -12
- data/lib/bioinform/support/strip_doc.rb +8 -8
- data/lib/bioinform/support/third_part/active_support/hash_with_indifferent_access.rb +3 -0
- data/lib/bioinform/support.rb +17 -17
- data/lib/bioinform/version.rb +3 -3
- data/lib/bioinform.rb +10 -10
- data/spec/cli/cli_spec.rb +13 -13
- data/spec/cli/convert_motif_spec.rb +106 -106
- data/spec/cli/data/merge_into_collection/GABPA_f1.pwm +14 -14
- data/spec/cli/data/merge_into_collection/KLF4_f2.pwm +11 -11
- data/spec/cli/data/merge_into_collection/SP1_f1.pwm +12 -12
- data/spec/cli/data/merge_into_collection/collection.txt.result +40 -40
- data/spec/cli/data/merge_into_collection/collection.yaml.result +188 -188
- data/spec/cli/data/merge_into_collection/collection_pwm.yaml.result +188 -188
- data/spec/cli/data/merge_into_collection/pwm_folder/GABPA_f1.pwm +14 -14
- data/spec/cli/data/merge_into_collection/pwm_folder/KLF4_f2.pwm +11 -11
- data/spec/cli/data/merge_into_collection/pwm_folder/SP1_f1.pwm +12 -12
- data/spec/cli/data/pcm2pwm/KLF4 f2 spaced name.pcm +11 -11
- data/spec/cli/data/pcm2pwm/KLF4_f2.pcm +11 -11
- data/spec/cli/data/pcm2pwm/KLF4_f2.pwm.result +11 -11
- data/spec/cli/data/pcm2pwm/SP1_f1.pcm +12 -12
- data/spec/cli/data/pcm2pwm/SP1_f1.pwm.result +12 -12
- data/spec/cli/data/split_motifs/GABPA_f1.mat.result +14 -14
- data/spec/cli/data/split_motifs/KLF4_f2.mat.result +11 -11
- data/spec/cli/data/split_motifs/SP1_f1.mat.result +12 -12
- data/spec/cli/data/split_motifs/collection.yaml +188 -188
- data/spec/cli/data/split_motifs/plain_collection.txt +38 -38
- data/spec/cli/merge_into_collection_spec.rb +99 -99
- data/spec/cli/pcm2pwm_spec.rb +79 -79
- data/spec/cli/shared_examples/convert_motif/motif_list_empty.rb +17 -17
- data/spec/cli/shared_examples/convert_motif/several_motifs_specified.rb +14 -14
- data/spec/cli/shared_examples/convert_motif/single_motif_specified.rb +49 -49
- data/spec/cli/shared_examples/convert_motif/yield_help_string.rb +4 -4
- data/spec/cli/shared_examples/convert_motif/yield_motif_conversion_error.rb +3 -3
- data/spec/cli/split_motifs_spec.rb +76 -76
- data/spec/data_models/collection_spec.rb +97 -97
- data/spec/data_models/motif_spec.rb +223 -223
- data/spec/data_models/pcm_spec.rb +55 -55
- data/spec/data_models/pm_spec.rb +359 -359
- data/spec/data_models/ppm_spec.rb +7 -7
- data/spec/data_models/pwm_spec.rb +82 -82
- data/spec/fabricators/collection_fabricator.rb +7 -7
- data/spec/fabricators/motif_fabricator.rb +32 -32
- data/spec/fabricators/motif_formats_fabricator.rb +124 -124
- data/spec/fabricators/pcm_fabricator.rb +24 -24
- data/spec/fabricators/pm_fabricator.rb +51 -51
- data/spec/fabricators/ppm_fabricator.rb +13 -13
- data/spec/fabricators/pwm_fabricator.rb +16 -16
- data/spec/parsers/parser_spec.rb +152 -152
- data/spec/parsers/string_fantom_parser_spec.rb +69 -69
- data/spec/parsers/string_parser_spec.rb +76 -76
- data/spec/parsers/trivial_parser_spec.rb +63 -63
- data/spec/parsers/yaml_parser_spec.rb +50 -50
- data/spec/spec_helper.rb +10 -10
- data/spec/spec_helper_source.rb +59 -59
- data/spec/support/advanced_scan_spec.rb +31 -31
- data/spec/support/array_product_spec.rb +14 -14
- data/spec/support/array_zip_spec.rb +14 -14
- data/spec/support/collect_hash_spec.rb +14 -14
- data/spec/support/delete_many_spec.rb +43 -43
- data/spec/support/inverf_spec.rb +18 -18
- data/spec/support/multiline_squish_spec.rb +24 -24
- data/spec/support/partial_sums_spec.rb +30 -30
- data/spec/support/same_by_spec.rb +35 -35
- metadata +3 -3
data/spec/data_models/pm_spec.rb
CHANGED
@@ -1,360 +1,360 @@
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require_relative '../spec_helper'
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require_relative '../../lib/bioinform/data_models/pm'
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module Bioinform
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describe PM do
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{:as_pcm => PCM, :as_pwm => PWM, :as_ppm => PPM}.each do |converter_method, result_klass|
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describe "##{converter_method}" do
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before :each do
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@collection = Collection.new(name: 'Collection 1')
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@matrix = [[1,2,3,4],[5,6,7,8]]
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@name = 'PM_motif'
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@background = [0.2,0.3,0.3,0.2]
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@tags = [@collection, 'Collection 2']
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@pm = PM.new(matrix: @matrix, name: @name, background: @background, tags: @tags)
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@conv_motif = @pm.send converter_method
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end
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it "should return an instance of #{result_klass}" do
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@conv_motif.should be_kind_of(result_klass)
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end
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it 'should return have the same matrix, name and background' do #, background and tags' do
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@conv_motif.matrix.should == @matrix
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@conv_motif.name.should == @name
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@conv_motif.background.should == @background
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# @conv_motif.tags.should == @tags
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end
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end
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end
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# describe '#tagged?' do
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# context 'when PM marked with Collection object' do
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# context 'without collection-name' do
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# before :each do
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# @marking_collection = Collection.new
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# @nonmarking_collection = Collection.new
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# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
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# @pm.mark(@marking_collection)
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# end
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# it 'should be true for marking collection' do
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# @pm.should be_tagged(@marking_collection)
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# end
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# it 'should be false for nonmarking collection' do
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# @pm.should_not be_tagged(@nonmarking_collection)
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# end
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# it 'should be false for nil-name' do
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# @pm.should_not be_tagged(nil)
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# end
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# it 'should be false for any string' do
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# @pm.should_not be_tagged('Another name')
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# end
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# end
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# context 'with collection-name' do
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# before :each do
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# @marking_collection = Collection.new(name: 'Collection name')
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# @nonmarking_collection = Collection.new(name: 'Another name')
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# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
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# @pm.mark(@marking_collection)
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# end
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# it 'should be true for marking collection' do
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# @pm.should be_tagged(@marking_collection)
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# end
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# it 'should be false for nonmarking collection' do
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# @pm.should_not be_tagged(@nonmarking_collection)
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# end
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# it 'should be true for name of marking collection' do
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# @pm.should be_tagged('Collection name')
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# end
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# it 'should be false for string that is not name of marking collection' do
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# @pm.should_not be_tagged('Another name')
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# end
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# end
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# end
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# context 'when PM marked with name' do
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# before :each do
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# @nonmarking_collection = Collection.new(name: 'Another name')
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# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
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# @pm.mark('Mark name')
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# end
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# it 'should be true for marking name' do
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# @pm.should be_tagged('Mark name')
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# end
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# it 'should be false for string that is not marking name' do
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# @pm.should_not be_tagged('Another name')
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# end
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# it 'should be false for nonmarking collection' do
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# @pm.should_not be_tagged(@nonmarking_collection)
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# end
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# end
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# context 'when PM marked with several marks' do
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# before :each do
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# @collection_1 = Collection.new(name: 'First name')
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# @collection_2 = Collection.new(name: 'Second name')
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# @collection_3 = Collection.new(name: 'Nonmarking collection')
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# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
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# @pm.mark(@collection_1)
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# @pm.mark(@collection_2)
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# @pm.mark('Stringy-name')
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# end
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# it 'should be true for each mark' do
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# @pm.should be_tagged(@collection_1)
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# @pm.should be_tagged(@collection_2)
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# @pm.should be_tagged('Stringy-name')
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# end
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# it 'should be false for not presented marks' do
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# @pm.should_not be_tagged(@collection_3)
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# @pm.should_not be_tagged('Bad stringy-name')
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# end
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# end
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# end
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describe '#==' do
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it 'should be true iff motifs have the same matrix, background and name' do
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pm = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif')
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pm_eq = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif')
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pm_neq_matrix = PM.new(matrix: [[1,2,3,4],[15,16,17,18]], name: 'First motif')
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pm_neq_name = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'Second motif')
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pm_neq_background = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif').set_parameters(background: [1,2,2,1])
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pm.should_not == pm_neq_matrix
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pm.should_not == pm_neq_name
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pm.should_not == pm_neq_background
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pm.should == pm_eq
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end
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end
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describe '::valid_matrix?' do
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it 'should be true iff an argument is an array of arrays of 4 numerics in a column' do
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PM.valid_matrix?( [[1,2,3,4],[1,4,5,6.5]] ).should be_true
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PM.valid_matrix?( {A: [1,1], C: [2,4], G: [3,5], T: [4, 6.5]} ).should be_false
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PM.valid_matrix?( [{A:1,C:2,G:3,T:4},{A:1,C:4,G:5,T: 6.5}] ).should be_false
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PM.valid_matrix?( [[1,2,3,4],[1,4,6.5]] ).should be_false
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PM.valid_matrix?( [[1,2,3],[1,4,6.5]] ).should be_false
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PM.valid_matrix?( [[1,2,'3','4'],[1,'4','5',6.5]] ).should be_false
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end
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end
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describe '#to_s' do
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before :each do
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@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
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end
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it 'should return string with single-tabulated multiline matrix' do
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@pm.to_s.should == "1\t2\t3\t4\n1\t4\t5\t6.5"
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end
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it 'should return positions in rows, letters in cols' do
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@pm.to_s.split("\n").size.should == 2
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@pm.to_s.split("\n").map{|pos| pos.split.size}.all?{|sz| sz==4}.should be_true
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end
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context 'with name specified' do
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before :each do
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@pm.name = 'Stub name'
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end
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it 'should return a string with a name and a matrix from the next line' do
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@pm.to_s.should == "Stub name\n1\t2\t3\t4\n1\t4\t5\t6.5"
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end
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it 'should not return a name if argument is set to false' do
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@pm.to_s(with_name: false).should == "1\t2\t3\t4\n1\t4\t5\t6.5"
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end
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end
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context 'in letters_as_rows mode' do
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it 'should print matrix with row-markers' do
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@pm.to_s(letters_as_rows: true).should == "A|1\t1\nC|2\t4\nG|3\t5\nT|4\t6.5"
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end
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end
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end
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describe '#pretty_string' do
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it 'should format string with 7-chars fields' do
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PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.should == " A C G T \n 1.0 2.0 3.0 4.0\n 5.0 6.0 7.0 8.0"
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end
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it 'should return a string of floats formatted with spaces' do
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PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.should match(/1.0 +2.0 +3.0 +4.0 *\n *5.0 +6.0 +7.0 +8.0/)
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end
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it 'should contain first string of ACGT letters' do
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PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.lines.first.should match(/A +C +G +T/)
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end
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it 'should round floats upto 3 digits' do
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PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] ).pretty_string.should match(/1.1 +2.22 +3.333 +4.444 *\n *5.5 +6.66 +7.777 +8.889/)
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end
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context 'with name specified' do
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before :each do
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@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
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@pm.name = 'MyName'
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end
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it 'should contain name if parameter `with_name` isn\'t false' do
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@pm.pretty_string.should match(/MyName\n/)
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end
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it 'should not contain name if parameter `with_name` is false' do
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@pm.pretty_string(with_name: false).should_not match(/MyName\n/)
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end
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end
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context 'without name specified' do
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before :each do
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@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
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end
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it 'should not contain name whether parameter `with_name` is or isn\'t false' do
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@pm.pretty_string.should_not match(/MyName\n/)
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@pm.pretty_string(with_name: false).should_not match(/MyName\n/)
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end
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end
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context 'in letters_as_rows mode' do
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it 'should print matrix with row-markers as to_s do' do
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@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
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@pm.pretty_string(letters_as_rows: true).should == @pm.to_s(letters_as_rows: true)
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end
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end
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end
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describe '#size' do
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it 'should return number of positions' do
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@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
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@pm.size.should == 2
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end
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end
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describe '#to_hash' do
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before :each do
|
218
|
-
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
219
|
-
@hsh = @pm.to_hash
|
220
|
-
end
|
221
|
-
it 'should return a hash with keys A, C, G, T' do
|
222
|
-
@hsh.should be_kind_of Hash
|
223
|
-
@hsh.keys.sort.should == %w{A C G T}
|
224
|
-
end
|
225
|
-
it 'should contain matrix elements of corresponding letter' do
|
226
|
-
@hsh['A'].should == [1, 1]
|
227
|
-
@hsh['C'].should == [2, 4]
|
228
|
-
@hsh['G'].should == [3, 5]
|
229
|
-
@hsh['T'].should == [4, 6.5]
|
230
|
-
end
|
231
|
-
it 'should be accessible both by name and symbol (e.g. pm.to_hash[:A] or pm.to_hash[\'A\'] is the same)' do
|
232
|
-
@hsh['A'].should == @hsh[:A]
|
233
|
-
@hsh['C'].should == @hsh[:C]
|
234
|
-
@hsh['G'].should == @hsh[:G]
|
235
|
-
@hsh['T'].should == @hsh[:T]
|
236
|
-
end
|
237
|
-
end
|
238
|
-
|
239
|
-
describe '#background' do
|
240
|
-
before :each do
|
241
|
-
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
242
|
-
end
|
243
|
-
context 'when pm just created' do
|
244
|
-
it 'should be [1,1,1,1]' do
|
245
|
-
@pm.background.should == [1,1,1,1]
|
246
|
-
end
|
247
|
-
end
|
248
|
-
end
|
249
|
-
|
250
|
-
describe '#reverse_complement!' do
|
251
|
-
before :each do
|
252
|
-
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
253
|
-
end
|
254
|
-
it 'should return pm object itself' do
|
255
|
-
@pm.reverse_complement!.should be_equal(@pm)
|
256
|
-
end
|
257
|
-
it 'should reverse matrix rows and columns' do
|
258
|
-
@pm.reverse_complement!
|
259
|
-
@pm.matrix.should == [[6.5, 5, 4, 1], [4, 3, 2, 1]]
|
260
|
-
end
|
261
|
-
end
|
262
|
-
|
263
|
-
describe '#left_augment!' do
|
264
|
-
before :each do
|
265
|
-
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
266
|
-
end
|
267
|
-
it 'should return pm object itself' do
|
268
|
-
@pm.left_augment!(2).should be_equal(@pm)
|
269
|
-
end
|
270
|
-
it 'should add number of zero columns from the left' do
|
271
|
-
@pm.left_augment!(2)
|
272
|
-
@pm.matrix.should == [[0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0], [1, 2, 3, 4], [1, 4, 5, 6.5]]
|
273
|
-
end
|
274
|
-
end
|
275
|
-
|
276
|
-
describe '#right_augment!' do
|
277
|
-
before :each do
|
278
|
-
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
279
|
-
end
|
280
|
-
it 'should return pm object itself' do
|
281
|
-
@pm.right_augment!(2).should be_equal(@pm)
|
282
|
-
end
|
283
|
-
it 'should add number of zero columns from the right' do
|
284
|
-
@pm.right_augment!(2)
|
285
|
-
@pm.matrix.should == [[1, 2, 3, 4], [1, 4, 5, 6.5], [0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0]]
|
286
|
-
end
|
287
|
-
end
|
288
|
-
|
289
|
-
describe '#discrete!' do
|
290
|
-
before :each do
|
291
|
-
@pm = PM.new( [[1.3, 2.0, 3.2, 4.9], [6.51, 6.5, 3.25, 4.633]] )
|
292
|
-
end
|
293
|
-
it 'should return pm object itself' do
|
294
|
-
@pm.discrete!(10).should be_equal(@pm)
|
295
|
-
end
|
296
|
-
context 'rate is 1' do
|
297
|
-
it 'should discrete each element of matrix' do
|
298
|
-
@pm.discrete!(1)
|
299
|
-
@pm.matrix.should == [[2, 2, 4, 5], [7, 7, 4, 5]]
|
300
|
-
end
|
301
|
-
end
|
302
|
-
it 'should discrete each element of matrix multiplied by rate' do
|
303
|
-
@pm.discrete!(10)
|
304
|
-
@pm.matrix.should == [[13, 20, 32, 49], [66, 65, 33, 47]]
|
305
|
-
end
|
306
|
-
end
|
307
|
-
|
308
|
-
describe '#vocabulary_volume' do
|
309
|
-
before :each do
|
310
|
-
@pm_2_positions = PM.new( [[1.3, 2.0, 3.2, 4.9], [5.0, 6.5, 3.2, 4.6]] )
|
311
|
-
@pm_3_positions = PM.new( [[1.3, 2.0, 3.2, 4.9], [5.0, 6.5, 3.2, 4.6], [1, 2, 3, 4]] )
|
312
|
-
end
|
313
|
-
context 'when background is [1,1,1,1]' do
|
314
|
-
it 'should be equal to number of words' do
|
315
|
-
@pm_2_positions.vocabulary_volume.should == 4**2
|
316
|
-
@pm_3_positions.vocabulary_volume.should == 4**3
|
317
|
-
end
|
318
|
-
end
|
319
|
-
context 'when background is normalized probabilities' do
|
320
|
-
it 'should be 1.0' do
|
321
|
-
@pm_2_positions.background = [0.2, 0.3, 0.3, 0.2]
|
322
|
-
@pm_2_positions.vocabulary_volume.should == 1.0
|
323
|
-
|
324
|
-
@pm_3_positions.background = [0.2, 0.3, 0.3, 0.2]
|
325
|
-
@pm_3_positions.vocabulary_volume.should == 1.0
|
326
|
-
end
|
327
|
-
end
|
328
|
-
end
|
329
|
-
|
330
|
-
[:reverse_complement].each do |meth|
|
331
|
-
describe "nonbang method #{meth}" do
|
332
|
-
before :each do
|
333
|
-
@pm = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
334
|
-
@pm_2 = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
335
|
-
end
|
336
|
-
it 'should return copy of object not object itself' do
|
337
|
-
@pm.send(meth).should_not be_equal @pm
|
338
|
-
end
|
339
|
-
it 'should == to bang-method' do
|
340
|
-
@pm.send(meth).to_s.should == @pm_2.send("#{meth}!").to_s
|
341
|
-
end
|
342
|
-
end
|
343
|
-
end
|
344
|
-
|
345
|
-
[:discrete , :left_augment, :right_augment].each do |meth|
|
346
|
-
describe "nonbang method #{meth}" do
|
347
|
-
before :each do
|
348
|
-
@pm = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
349
|
-
@pm_2 = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
350
|
-
end
|
351
|
-
it 'should return copy of object not object itself' do
|
352
|
-
@pm.send(meth, 2).should_not be_equal @pm
|
353
|
-
end
|
354
|
-
it 'should == to bang-method' do
|
355
|
-
@pm.send(meth, 2).to_s.should == @pm_2.send("#{meth}!", 2).to_s
|
356
|
-
end
|
357
|
-
end
|
358
|
-
end
|
359
|
-
end
|
1
|
+
require_relative '../spec_helper'
|
2
|
+
require_relative '../../lib/bioinform/data_models/pm'
|
3
|
+
|
4
|
+
module Bioinform
|
5
|
+
describe PM do
|
6
|
+
{:as_pcm => PCM, :as_pwm => PWM, :as_ppm => PPM}.each do |converter_method, result_klass|
|
7
|
+
describe "##{converter_method}" do
|
8
|
+
before :each do
|
9
|
+
@collection = Collection.new(name: 'Collection 1')
|
10
|
+
@matrix = [[1,2,3,4],[5,6,7,8]]
|
11
|
+
@name = 'PM_motif'
|
12
|
+
@background = [0.2,0.3,0.3,0.2]
|
13
|
+
@tags = [@collection, 'Collection 2']
|
14
|
+
@pm = PM.new(matrix: @matrix, name: @name, background: @background, tags: @tags)
|
15
|
+
@conv_motif = @pm.send converter_method
|
16
|
+
end
|
17
|
+
it "should return an instance of #{result_klass}" do
|
18
|
+
@conv_motif.should be_kind_of(result_klass)
|
19
|
+
end
|
20
|
+
it 'should return have the same matrix, name and background' do #, background and tags' do
|
21
|
+
@conv_motif.matrix.should == @matrix
|
22
|
+
@conv_motif.name.should == @name
|
23
|
+
@conv_motif.background.should == @background
|
24
|
+
# @conv_motif.tags.should == @tags
|
25
|
+
end
|
26
|
+
end
|
27
|
+
end
|
28
|
+
|
29
|
+
# describe '#tagged?' do
|
30
|
+
# context 'when PM marked with Collection object' do
|
31
|
+
# context 'without collection-name' do
|
32
|
+
# before :each do
|
33
|
+
# @marking_collection = Collection.new
|
34
|
+
# @nonmarking_collection = Collection.new
|
35
|
+
# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
|
36
|
+
# @pm.mark(@marking_collection)
|
37
|
+
# end
|
38
|
+
# it 'should be true for marking collection' do
|
39
|
+
# @pm.should be_tagged(@marking_collection)
|
40
|
+
# end
|
41
|
+
# it 'should be false for nonmarking collection' do
|
42
|
+
# @pm.should_not be_tagged(@nonmarking_collection)
|
43
|
+
# end
|
44
|
+
# it 'should be false for nil-name' do
|
45
|
+
# @pm.should_not be_tagged(nil)
|
46
|
+
# end
|
47
|
+
# it 'should be false for any string' do
|
48
|
+
# @pm.should_not be_tagged('Another name')
|
49
|
+
# end
|
50
|
+
# end
|
51
|
+
# context 'with collection-name' do
|
52
|
+
# before :each do
|
53
|
+
# @marking_collection = Collection.new(name: 'Collection name')
|
54
|
+
# @nonmarking_collection = Collection.new(name: 'Another name')
|
55
|
+
# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
|
56
|
+
# @pm.mark(@marking_collection)
|
57
|
+
# end
|
58
|
+
# it 'should be true for marking collection' do
|
59
|
+
# @pm.should be_tagged(@marking_collection)
|
60
|
+
# end
|
61
|
+
# it 'should be false for nonmarking collection' do
|
62
|
+
# @pm.should_not be_tagged(@nonmarking_collection)
|
63
|
+
# end
|
64
|
+
# it 'should be true for name of marking collection' do
|
65
|
+
# @pm.should be_tagged('Collection name')
|
66
|
+
# end
|
67
|
+
# it 'should be false for string that is not name of marking collection' do
|
68
|
+
# @pm.should_not be_tagged('Another name')
|
69
|
+
# end
|
70
|
+
# end
|
71
|
+
# end
|
72
|
+
|
73
|
+
# context 'when PM marked with name' do
|
74
|
+
# before :each do
|
75
|
+
# @nonmarking_collection = Collection.new(name: 'Another name')
|
76
|
+
# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
|
77
|
+
# @pm.mark('Mark name')
|
78
|
+
# end
|
79
|
+
# it 'should be true for marking name' do
|
80
|
+
# @pm.should be_tagged('Mark name')
|
81
|
+
# end
|
82
|
+
# it 'should be false for string that is not marking name' do
|
83
|
+
# @pm.should_not be_tagged('Another name')
|
84
|
+
# end
|
85
|
+
# it 'should be false for nonmarking collection' do
|
86
|
+
# @pm.should_not be_tagged(@nonmarking_collection)
|
87
|
+
# end
|
88
|
+
# end
|
89
|
+
|
90
|
+
# context 'when PM marked with several marks' do
|
91
|
+
# before :each do
|
92
|
+
# @collection_1 = Collection.new(name: 'First name')
|
93
|
+
# @collection_2 = Collection.new(name: 'Second name')
|
94
|
+
# @collection_3 = Collection.new(name: 'Nonmarking collection')
|
95
|
+
# @pm = PM.new(matrix:[[1,1,1,1]], name:'Motif name')
|
96
|
+
# @pm.mark(@collection_1)
|
97
|
+
# @pm.mark(@collection_2)
|
98
|
+
# @pm.mark('Stringy-name')
|
99
|
+
# end
|
100
|
+
# it 'should be true for each mark' do
|
101
|
+
# @pm.should be_tagged(@collection_1)
|
102
|
+
# @pm.should be_tagged(@collection_2)
|
103
|
+
# @pm.should be_tagged('Stringy-name')
|
104
|
+
# end
|
105
|
+
# it 'should be false for not presented marks' do
|
106
|
+
# @pm.should_not be_tagged(@collection_3)
|
107
|
+
# @pm.should_not be_tagged('Bad stringy-name')
|
108
|
+
# end
|
109
|
+
# end
|
110
|
+
# end
|
111
|
+
|
112
|
+
describe '#==' do
|
113
|
+
it 'should be true iff motifs have the same matrix, background and name' do
|
114
|
+
pm = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif')
|
115
|
+
pm_eq = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif')
|
116
|
+
pm_neq_matrix = PM.new(matrix: [[1,2,3,4],[15,16,17,18]], name: 'First motif')
|
117
|
+
pm_neq_name = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'Second motif')
|
118
|
+
pm_neq_background = PM.new(matrix: [[1,2,3,4],[5,6,7,8]], name: 'First motif').set_parameters(background: [1,2,2,1])
|
119
|
+
|
120
|
+
pm.should_not == pm_neq_matrix
|
121
|
+
pm.should_not == pm_neq_name
|
122
|
+
pm.should_not == pm_neq_background
|
123
|
+
pm.should == pm_eq
|
124
|
+
end
|
125
|
+
end
|
126
|
+
describe '::valid_matrix?' do
|
127
|
+
it 'should be true iff an argument is an array of arrays of 4 numerics in a column' do
|
128
|
+
PM.valid_matrix?( [[1,2,3,4],[1,4,5,6.5]] ).should be_true
|
129
|
+
PM.valid_matrix?( {A: [1,1], C: [2,4], G: [3,5], T: [4, 6.5]} ).should be_false
|
130
|
+
PM.valid_matrix?( [{A:1,C:2,G:3,T:4},{A:1,C:4,G:5,T: 6.5}] ).should be_false
|
131
|
+
PM.valid_matrix?( [[1,2,3,4],[1,4,6.5]] ).should be_false
|
132
|
+
PM.valid_matrix?( [[1,2,3],[1,4,6.5]] ).should be_false
|
133
|
+
PM.valid_matrix?( [[1,2,'3','4'],[1,'4','5',6.5]] ).should be_false
|
134
|
+
end
|
135
|
+
end
|
136
|
+
|
137
|
+
describe '#to_s' do
|
138
|
+
before :each do
|
139
|
+
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
140
|
+
end
|
141
|
+
it 'should return string with single-tabulated multiline matrix' do
|
142
|
+
@pm.to_s.should == "1\t2\t3\t4\n1\t4\t5\t6.5"
|
143
|
+
end
|
144
|
+
it 'should return positions in rows, letters in cols' do
|
145
|
+
@pm.to_s.split("\n").size.should == 2
|
146
|
+
@pm.to_s.split("\n").map{|pos| pos.split.size}.all?{|sz| sz==4}.should be_true
|
147
|
+
end
|
148
|
+
context 'with name specified' do
|
149
|
+
before :each do
|
150
|
+
@pm.name = 'Stub name'
|
151
|
+
end
|
152
|
+
it 'should return a string with a name and a matrix from the next line' do
|
153
|
+
@pm.to_s.should == "Stub name\n1\t2\t3\t4\n1\t4\t5\t6.5"
|
154
|
+
end
|
155
|
+
it 'should not return a name if argument is set to false' do
|
156
|
+
@pm.to_s(with_name: false).should == "1\t2\t3\t4\n1\t4\t5\t6.5"
|
157
|
+
end
|
158
|
+
end
|
159
|
+
context 'in letters_as_rows mode' do
|
160
|
+
it 'should print matrix with row-markers' do
|
161
|
+
@pm.to_s(letters_as_rows: true).should == "A|1\t1\nC|2\t4\nG|3\t5\nT|4\t6.5"
|
162
|
+
end
|
163
|
+
end
|
164
|
+
end
|
165
|
+
|
166
|
+
describe '#pretty_string' do
|
167
|
+
it 'should format string with 7-chars fields' do
|
168
|
+
PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.should == " A C G T \n 1.0 2.0 3.0 4.0\n 5.0 6.0 7.0 8.0"
|
169
|
+
end
|
170
|
+
it 'should return a string of floats formatted with spaces' do
|
171
|
+
PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.should match(/1.0 +2.0 +3.0 +4.0 *\n *5.0 +6.0 +7.0 +8.0/)
|
172
|
+
end
|
173
|
+
it 'should contain first string of ACGT letters' do
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174
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+
PM.new( [[1,2,3,4],[5,6,7,8]] ).pretty_string.lines.first.should match(/A +C +G +T/)
|
175
|
+
end
|
176
|
+
it 'should round floats upto 3 digits' do
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177
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+
PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] ).pretty_string.should match(/1.1 +2.22 +3.333 +4.444 *\n *5.5 +6.66 +7.777 +8.889/)
|
178
|
+
end
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179
|
+
|
180
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+
context 'with name specified' do
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+
before :each do
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182
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+
@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
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183
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+
@pm.name = 'MyName'
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184
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+
end
|
185
|
+
it 'should contain name if parameter `with_name` isn\'t false' do
|
186
|
+
@pm.pretty_string.should match(/MyName\n/)
|
187
|
+
end
|
188
|
+
it 'should not contain name if parameter `with_name` is false' do
|
189
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+
@pm.pretty_string(with_name: false).should_not match(/MyName\n/)
|
190
|
+
end
|
191
|
+
end
|
192
|
+
context 'without name specified' do
|
193
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+
before :each do
|
194
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+
@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
|
195
|
+
end
|
196
|
+
it 'should not contain name whether parameter `with_name` is or isn\'t false' do
|
197
|
+
@pm.pretty_string.should_not match(/MyName\n/)
|
198
|
+
@pm.pretty_string(with_name: false).should_not match(/MyName\n/)
|
199
|
+
end
|
200
|
+
end
|
201
|
+
context 'in letters_as_rows mode' do
|
202
|
+
it 'should print matrix with row-markers as to_s do' do
|
203
|
+
@pm = PM.new( [[1.1,2.22,3.333,4.4444],[5.5,6.66,7.777,8.8888]] )
|
204
|
+
@pm.pretty_string(letters_as_rows: true).should == @pm.to_s(letters_as_rows: true)
|
205
|
+
end
|
206
|
+
end
|
207
|
+
end
|
208
|
+
|
209
|
+
describe '#size' do
|
210
|
+
it 'should return number of positions' do
|
211
|
+
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
212
|
+
@pm.size.should == 2
|
213
|
+
end
|
214
|
+
end
|
215
|
+
|
216
|
+
describe '#to_hash' do
|
217
|
+
before :each do
|
218
|
+
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
219
|
+
@hsh = @pm.to_hash
|
220
|
+
end
|
221
|
+
it 'should return a hash with keys A, C, G, T' do
|
222
|
+
@hsh.should be_kind_of Hash
|
223
|
+
@hsh.keys.sort.should == %w{A C G T}
|
224
|
+
end
|
225
|
+
it 'should contain matrix elements of corresponding letter' do
|
226
|
+
@hsh['A'].should == [1, 1]
|
227
|
+
@hsh['C'].should == [2, 4]
|
228
|
+
@hsh['G'].should == [3, 5]
|
229
|
+
@hsh['T'].should == [4, 6.5]
|
230
|
+
end
|
231
|
+
it 'should be accessible both by name and symbol (e.g. pm.to_hash[:A] or pm.to_hash[\'A\'] is the same)' do
|
232
|
+
@hsh['A'].should == @hsh[:A]
|
233
|
+
@hsh['C'].should == @hsh[:C]
|
234
|
+
@hsh['G'].should == @hsh[:G]
|
235
|
+
@hsh['T'].should == @hsh[:T]
|
236
|
+
end
|
237
|
+
end
|
238
|
+
|
239
|
+
describe '#background' do
|
240
|
+
before :each do
|
241
|
+
@pm = PM.new( [[1,2,3,4],[1,4,5,6.5]] )
|
242
|
+
end
|
243
|
+
context 'when pm just created' do
|
244
|
+
it 'should be [1,1,1,1]' do
|
245
|
+
@pm.background.should == [1,1,1,1]
|
246
|
+
end
|
247
|
+
end
|
248
|
+
end
|
249
|
+
|
250
|
+
describe '#reverse_complement!' do
|
251
|
+
before :each do
|
252
|
+
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
253
|
+
end
|
254
|
+
it 'should return pm object itself' do
|
255
|
+
@pm.reverse_complement!.should be_equal(@pm)
|
256
|
+
end
|
257
|
+
it 'should reverse matrix rows and columns' do
|
258
|
+
@pm.reverse_complement!
|
259
|
+
@pm.matrix.should == [[6.5, 5, 4, 1], [4, 3, 2, 1]]
|
260
|
+
end
|
261
|
+
end
|
262
|
+
|
263
|
+
describe '#left_augment!' do
|
264
|
+
before :each do
|
265
|
+
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
266
|
+
end
|
267
|
+
it 'should return pm object itself' do
|
268
|
+
@pm.left_augment!(2).should be_equal(@pm)
|
269
|
+
end
|
270
|
+
it 'should add number of zero columns from the left' do
|
271
|
+
@pm.left_augment!(2)
|
272
|
+
@pm.matrix.should == [[0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0], [1, 2, 3, 4], [1, 4, 5, 6.5]]
|
273
|
+
end
|
274
|
+
end
|
275
|
+
|
276
|
+
describe '#right_augment!' do
|
277
|
+
before :each do
|
278
|
+
@pm = PM.new( [[1, 2, 3, 4], [1, 4, 5, 6.5]] )
|
279
|
+
end
|
280
|
+
it 'should return pm object itself' do
|
281
|
+
@pm.right_augment!(2).should be_equal(@pm)
|
282
|
+
end
|
283
|
+
it 'should add number of zero columns from the right' do
|
284
|
+
@pm.right_augment!(2)
|
285
|
+
@pm.matrix.should == [[1, 2, 3, 4], [1, 4, 5, 6.5], [0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0]]
|
286
|
+
end
|
287
|
+
end
|
288
|
+
|
289
|
+
describe '#discrete!' do
|
290
|
+
before :each do
|
291
|
+
@pm = PM.new( [[1.3, 2.0, 3.2, 4.9], [6.51, 6.5, 3.25, 4.633]] )
|
292
|
+
end
|
293
|
+
it 'should return pm object itself' do
|
294
|
+
@pm.discrete!(10).should be_equal(@pm)
|
295
|
+
end
|
296
|
+
context 'rate is 1' do
|
297
|
+
it 'should discrete each element of matrix' do
|
298
|
+
@pm.discrete!(1)
|
299
|
+
@pm.matrix.should == [[2, 2, 4, 5], [7, 7, 4, 5]]
|
300
|
+
end
|
301
|
+
end
|
302
|
+
it 'should discrete each element of matrix multiplied by rate' do
|
303
|
+
@pm.discrete!(10)
|
304
|
+
@pm.matrix.should == [[13, 20, 32, 49], [66, 65, 33, 47]]
|
305
|
+
end
|
306
|
+
end
|
307
|
+
|
308
|
+
describe '#vocabulary_volume' do
|
309
|
+
before :each do
|
310
|
+
@pm_2_positions = PM.new( [[1.3, 2.0, 3.2, 4.9], [5.0, 6.5, 3.2, 4.6]] )
|
311
|
+
@pm_3_positions = PM.new( [[1.3, 2.0, 3.2, 4.9], [5.0, 6.5, 3.2, 4.6], [1, 2, 3, 4]] )
|
312
|
+
end
|
313
|
+
context 'when background is [1,1,1,1]' do
|
314
|
+
it 'should be equal to number of words' do
|
315
|
+
@pm_2_positions.vocabulary_volume.should == 4**2
|
316
|
+
@pm_3_positions.vocabulary_volume.should == 4**3
|
317
|
+
end
|
318
|
+
end
|
319
|
+
context 'when background is normalized probabilities' do
|
320
|
+
it 'should be 1.0' do
|
321
|
+
@pm_2_positions.background = [0.2, 0.3, 0.3, 0.2]
|
322
|
+
@pm_2_positions.vocabulary_volume.should == 1.0
|
323
|
+
|
324
|
+
@pm_3_positions.background = [0.2, 0.3, 0.3, 0.2]
|
325
|
+
@pm_3_positions.vocabulary_volume.should == 1.0
|
326
|
+
end
|
327
|
+
end
|
328
|
+
end
|
329
|
+
|
330
|
+
[:reverse_complement].each do |meth|
|
331
|
+
describe "nonbang method #{meth}" do
|
332
|
+
before :each do
|
333
|
+
@pm = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
334
|
+
@pm_2 = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
335
|
+
end
|
336
|
+
it 'should return copy of object not object itself' do
|
337
|
+
@pm.send(meth).should_not be_equal @pm
|
338
|
+
end
|
339
|
+
it 'should == to bang-method' do
|
340
|
+
@pm.send(meth).to_s.should == @pm_2.send("#{meth}!").to_s
|
341
|
+
end
|
342
|
+
end
|
343
|
+
end
|
344
|
+
|
345
|
+
[:discrete , :left_augment, :right_augment].each do |meth|
|
346
|
+
describe "nonbang method #{meth}" do
|
347
|
+
before :each do
|
348
|
+
@pm = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
349
|
+
@pm_2 = PM.new( [[1.3, 2.0, 4.9, 3.2], [7.13, 6.5, 3.25, 4.633], [-1.0, -1.0, -1.5, -1.0]] )
|
350
|
+
end
|
351
|
+
it 'should return copy of object not object itself' do
|
352
|
+
@pm.send(meth, 2).should_not be_equal @pm
|
353
|
+
end
|
354
|
+
it 'should == to bang-method' do
|
355
|
+
@pm.send(meth, 2).to_s.should == @pm_2.send("#{meth}!", 2).to_s
|
356
|
+
end
|
357
|
+
end
|
358
|
+
end
|
359
|
+
end
|
360
360
|
end
|