bioinform 0.1.17 → 0.2.0

data/spec/parsers/trivial_parser_spec.rb

@@ -1,64 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/parsers/parser'
-require_relative '../../lib/bioinform/data_models/collection'
-
-module Bioinform
-  describe TrivialParser do
-    context '.new' do
-      it 'should take the only input argument' do
-        TrivialParser.instance_method(:initialize).arity.should == 1
-      end
-    end
-
-    context '#parse!' do
-      it 'should return OpenStruct based on input of that was passed to initialize when input is a Hash' do
-        TrivialParser.new(matrix: 'stub matrix', name: 'stub name').parse!.should == OpenStruct.new(matrix: 'stub matrix', name: 'stub name')
-      end
-
-      it 'should return OpenStruct based on input of that was passed to initialize when input is a OpenStruct' do
-        TrivialParser.new(OpenStruct.new(matrix: 'stub matrix', name: 'stub name')).parse!.should == OpenStruct.new(matrix: 'stub matrix', name: 'stub name')
-      end
-    end
-
-    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
-    end
-
-    it 'can be used to create PM with {matrix: ..., name: ...} form' do
-      pm = PM.new({matrix: [[1,2,3,4],[5,6,7,8]], name: 'Name'}, TrivialParser)
-      pm.matrix.should == [[1,2,3,4],[5,6,7,8]]
-      pm.name.should == 'Name'
-    end
-
-    it 'can be used to create PM from PM (make copy)' do
-      pm = Fabricate(:pm)
-      pm_copy = PM.new(pm, TrivialParser)
-      pm_copy.should == pm
-    end
-  end
-
-  describe TrivialCollectionParser do
-    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.parse!.should == pm_3
-        expect{ @parser.parse! }.to raise_error
-      end
-    end
-
-    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, pm_3]
-      end
-    end
-  end
-end

data/spec/parsers/yaml_parser_spec.rb

@@ -1,50 +0,0 @@
-require 'yaml'
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/parsers/yaml_parser'
-require_relative '../../lib/bioinform/data_models/collection'
-
-module Bioinform
-  describe YAMLParser do
-    context '#parse!' do
-      it 'should return PM that was encoded in YAML format' do
-        pm = Fabricate(:pm)
-        parser = YAMLParser.new(pm.to_yaml)
-        parser.parse!.should == pm
-      end
-    end
-    it 'can be used to create PM from yaml-string' do
-      pm = Fabricate(:pm)
-      pm_copy = PM.new(pm.to_yaml, YAMLParser)
-      pm_copy.should == pm
-    end
-
-    context '::split_on_motifs' do
-      it 'should be able to get a single PM' do
-        pm = Fabricate(:pm)
-        YAMLParser.split_on_motifs(pm.to_yaml, PM).should == [ pm ]
-      end
-    end
-  end
-
-  describe YAMLCollectionParser do
-    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 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(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
-  end
-end

data/spec/support/advanced_scan_spec.rb

@@ -1,32 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/advanced_scan'
-
-describe StringScanner do
-  context '#advanced_scan' do
-    before do
-      @scanner = StringScanner.new('abcde  fghIJKLmnop')
-    end
-    it 'should return nil if text doesn\'t match. Pointer should not move' do
-      @scanner.advanced_scan(/\s\s\s/).should be_nil
-      @scanner.pos.should == 0
-    end
-    it 'should return MatchData if string Matches. Pointer should move' do
-      @scanner.advanced_scan(/\w\w\w/).should be_kind_of MatchData
-      @scanner.pos.should == 3
-    end
-    it 'should return have the same groups as regexp has' do
-      result = @scanner.advanced_scan(/(\w+)(\s+)([a-z]+)([A-Z]+)/)
-      result[0].should == 'abcde  fghIJKL'
-      result[1].should == 'abcde'
-      result[2].should == '  '
-      result[3].should == 'fgh'
-      result[4].should == 'IJKL'
-    end
-    it 'should return have the same named groups as regexp has' do
-      result = @scanner.advanced_scan(/(\w+)(\s+)(?<word_downcase>[a-z]+)(?<word_upcase>[A-Z]+)/)
-      result[0].should == 'abcde  fghIJKL'
-      result[:word_downcase].should == 'fgh'
-      result[:word_upcase].should == 'IJKL'
-    end
-  end
-end

data/spec/support/array_product_spec.rb

@@ -1,15 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/array_product'
-
-describe Array do
-  context '::product' do
-    it 'should take any number of arrays and product them as if #product was made to first and others' do
-      Array.product([1,2,3]).should == [1,2,3].product()
-      Array.product([1,2,3],[4,5,6]).should == [1,2,3].product([4,5,6])
-      Array.product([1,2,3],[4,5,6],[7,8,9]).should == [1,2,3].product([4,5,6],[7,8,9])
-    end
-    it 'should return empty array if no arrays\'re given' do
-      Array.product().should == []
-    end
-  end
-end

data/spec/support/array_zip_spec.rb

@@ -1,15 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/array_zip'
-
-describe Array do
-  context '::zip' do
-    it 'should take any number of arrays and zip them as if #zip was made to first and others' do
-      Array.zip([1,2,3]).should == [1,2,3].zip()
-      Array.zip([1,2,3],[4,5,6]).should == [1,2,3].zip([4,5,6])
-      Array.zip([1,2,3],[4,5,6],[7,8,9]).should == [1,2,3].zip([4,5,6],[7,8,9])
-    end
-    it 'should return empty array if no arrays\'re given' do
-      Array.zip().should == []
-    end
-  end
-end

data/spec/support/collect_hash_spec.rb

@@ -1,15 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/collect_hash'
-
-describe Enumerable do
-  # %w{A C G T}.collect_hash{|k| [k*2, k*3] }
-  # # ==> {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-  context '#collect_hash' do
-    it 'should take a block and create a hash from collected [k,v] pairs' do
-      %w{A C G T}.collect_hash{|k| [k*2, k*3] }.should == {"AA" => "AAA", "CC" => "CCC", "GG" => "GGG", "TT" => "TTT"}
-    end
-    it 'should create a hash from yielded [k,v] pairs if block not given' do
-      %w{A C G T}.each_with_index.collect_hash.should == {"A" => 0, "C" => 1, "G" => 2, "T" => 3}
-    end
-  end
-end

data/spec/support/delete_many_spec.rb

@@ -1,44 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/delete_many'
-
-describe Array do
-  before :each do
-    @arr = %w{a b c d e f g h i j b b}
-  end
-  describe '#delete_at_many' do
-    it 'should delete elements at specified indices when indices in ascending order' do
-      @arr.delete_at_many(1,3,7)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete elements at specified indices when indices in descending order' do
-      @arr.delete_at_many(7,3,1)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete elements at specified indices when indices in arbitrary order' do
-      @arr.delete_at_many(3,1,7)
-      @arr.should == %w{a c e f g i j b b}
-    end
-    it 'should delete at each index once' do
-      @arr.delete_at_many(0,0,0,2,0)
-      @arr.should == %w{b d e f g h i j b b}
-    end
-  end
-  describe '#delete_many' do
-    it 'should delete multiple elements with specified values' do
-      @arr.delete_many('b', 'd', 'h', 'b')
-      @arr.should == %w{a c e f g i j}
-    end
-  end
-end
-
-describe Hash do
-  before :each do
-    @arr = {A: 3, T: 6, G: 4, C: 5}
-  end
-  describe '#delete_many' do
-    it 'should delete specified keys' do
-      @arr.delete_many(:T, :C, :F, :T, :T)
-      @arr.should == {A: 3, G: 4}
-    end
-  end
-end

data/spec/support/inverf_spec.rb

@@ -1,19 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/inverf'
-
-describe 'Math#inverf' do
-  it 'should be erf(inverf(x)) == x' do
-    rng = (-0.9..0.9).step(0.1)
-    arr = rng.to_a
-    arr2 = rng.map{|x| Math.inverf(x)}.map{|x| Math.erf(x)}
-    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
-    delta.each{|el| el.should <= 0.001}
-  end
-  it 'should be erf(inverf(x)) == x' do
-    rng = (-5..5).step(1)
-    arr = rng.to_a
-    arr2 = rng.map{|x| Math.erf(x)}.map{|x| Math.inverf(x)}
-    delta = arr.each_index.map{|i| (arr[i] - arr2[i]).abs }
-    delta.each{|el| el.should <= 0.01}
-  end
-end

data/spec/support/multiline_squish_spec.rb

@@ -1,25 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/multiline_squish'
-
-describe String do
-  describe '#multiline_squish' do
-    it 'should replace multiple spaces with one space' do
-      "abc def   ghi\n  jk  lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should replace tabs with a space' do
-      "abc\tdef   ghi \t jk".multiline_squish.should == 'abc def ghi jk'
-    end
-    it 'should replace \r\n with \n' do
-      "abc def ghi\r\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should preserve rows pagination' do
-      "abc def ghi\njk lmn".multiline_squish.should == "abc def ghi\njk lmn"
-    end
-    it 'should preserve empty lines in the middle of text' do
-      "abc def\n\nghi\n \t  \njk lmn \n\n\n zzz".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
-    end
-    it 'should drop empty lines at begin and at end of string' do
-      "\n  \t\n\nabc def\n\nghi\n \t  \njk lmn \n\n\n zzz\n\n \t  \n".multiline_squish.should == "abc def\n\nghi\n\njk lmn\n\n\nzzz"
-    end
-  end
-end

data/spec/support/partial_sums_spec.rb

@@ -1,30 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/partial_sums'
-
-describe 'Array#partial_sums' do
-  context 'when no initial value given' do
-    it 'should return an array of the same size with partial sums of elements 0..ind inclusive with float elements' do
-      [2,3,4,5].partial_sums.should == [2, 5, 9, 14]
-      [2,3,4,5].partial_sums.last.should be_kind_of(Float)
-    end
-  end
-  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
-    [2,3,4,5].partial_sums(100).should == [102,105,109,114]
-    [2,3,4,5].partial_sums(100).last.should be_kind_of(Integer)
-  end
-end
-
-{1 => 5, 4 => 3, 3 => 2}.partial_sums == {1=>5, 3=>7, 4=>10}
-
-describe 'Hash#partial_sums' do
-  context 'when no initial value given' do
-    it 'should return a hash with float values of the same size with partial sums of elements that has keys <= than argument' do
-      {1 => 5, 4 => 3, 3 => 2}.partial_sums.should == {1=>5, 3=>7, 4=>10}
-      {1 => 5, 4 => 3, 3 => 2}.partial_sums.values.last.should be_kind_of(Float)
-    end
-  end
-  it 'should start counting from argument when it\'s given. Type of values depends on type of initial value' do
-    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).should == {1=>105, 3=>107, 4=>110}
-    {1 => 5, 4 => 3, 3 => 2}.partial_sums(100).values.last.should be_kind_of(Integer)
-  end
-end

data/spec/support/same_by_spec.rb

@@ -1,36 +0,0 @@
-require_relative '../spec_helper'
-require_relative '../../lib/bioinform/support/same_by'
-
-describe Enumerable do
-  describe '#same_by?' do
-    it 'should be work with both hashes and arrays' do
-      ['a','b','c'].same_by?{|k| k.length}
-      {'a'=>13,'b'=>12,'c'=>14}.same_by?{|k,v| v < 20}
-    end
-    it 'should be true for empty collections' do
-      [].same_by?(&:length).should be_true
-      [].same_by?.should be_true
-    end
-    context 'without block' do
-      it 'should compare if all elements of collection are the same' do
-        %w{cat cat cat}.same_by?.should be_true
-        %w{cat dog rat}.same_by?.should be_false
-      end
-    end
-    context 'with a block' do
-      it 'should compare enumerables by a value of block' do
-        %w{cat dog rat}.same_by?(&:length).should be_true
-        %w{cat dog rabbit}.same_by?(&:length).should be_false
-      end
-      it 'should be true if all elements are true' do
-        [4,8,2,2].same_by?(&:even?).should be_true
-      end
-      it 'should be true if all elements are false' do
-        [1,3,9,7].same_by?(&:even?).should be_true
-      end
-      it 'should be false if some elements are true and some are false' do
-        [1,8,3,2].same_by?(&:even?).should be_false
-      end
-    end
-  end
-end