macroape 3.2.2 → 3.3.0

data/lib/macroape/single_matrix.rb

@@ -1,45 +0,0 @@
-module PWM
-  class SingleMatrix
-    attr_reader :matrix
-    attr_accessor :name
-    def initialize(matrix)
-      @matrix = matrix
-    end
-    include MatrixTransformations, MatrixInformation
-    
-    def self.build_matrix(lines, name = nil)
-      pwm_name = name
-      begin
-        lines.first.split.each{|x| Float(x) }
-        start_line = 0
-      rescue
-        start_line = 1
-        pwm_name = lines.first.chomp.match(/(?:>\s)?(.*)$/)[1]
-      end
-      
-      if lines[start_line].split.length == 4
-        pwm = SingleMatrix.new(lines[start_line..-1].map{|str| str.split.map(&:to_f)})
-      else
-        pwm = SingleMatrix.new(lines[start_line..-1].map{|str| str.split.map(&:to_f)}.transpose)
-      end
-      raise "PWM::SingleMatrix.build_matrix can't create matrix using this input" unless pwm.matrix.all?{|l| l.length == 4}
-      pwm.name = pwm_name
-      pwm
-    end
-    
-    def self.load_from_stdin(input_stream, name = nil)
-      build_matrix(input_stream.readlines, name)
-    end
-    def self.load_from_line_array(lines, name = nil)
-      build_matrix(lines, name)
-    end
-    
-    def self.load_pat(filename)
-      build_matrix( File.open(filename,'r'){|f| f.readlines}, File.basename_wo_ext(filename))
-    end
-    
-    def with_background(background)
-      type_cast(MatrixOnBackground){@probabilities = background}.depth_dup
-    end
-  end
-end

data/lib/macroape/support.rb

@@ -1,34 +0,0 @@
-module Kernel
-  def type_cast(new_class, &block)
-    new_obj = new_class.allocate  
-    instance_variables.each do |varname|
-      new_obj.instance_variable_set(varname, self.instance_variable_get(varname))
-    end
-    new_obj.instance_eval(&block) if block_given?
-    new_obj
-  end
-  
-  def depth_dup
-    begin
-      new_obj = self.dup
-    rescue
-      return self
-    end
-    new_obj.instance_variables.each do |varname|
-      begin
-        new_obj.instance_variable_set(varname, new_obj.instance_variable_get(varname).depth_dup)
-      rescue
-      end
-    end
-    new_obj
-  end
-  
-end
-
-def File.filename_wo_ext(filename)
-  filename[0..-(1+File.extname(filename).length)]
-end
-
-def File.basename_wo_ext(filename)
-  File.basename(filename)[0..-(1+File.extname(filename).length)]
-end

data/test/macroape_test.rb

@@ -1,125 +0,0 @@
-require 'test/unit'
-
-module Helpers
-  def self.obtain_pvalue_by_threshold(args)
-    IO.popen("find_pvalue #{args}",&:read).strip.split.last
-  end
-end
-
-class FindThresholdTest < Test::Unit::TestCase
-  def test_process_several_pvalues
-    pvalues = []
-    IO.popen('find_threshold test/data/KLF4_f2.pat -p 0.001 0.0005', &:read).lines.each{|line| 
-      pvalue, threshold, real_pvalue = line.strip.split("\t")
-      pvalues << pvalue
-      assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
-    }
-    assert_equal pvalues, ['0.0005', '0.001']
-  end
-  def test_process_one_pvalue
-    pvalue, threshold, real_pvalue = IO.popen('find_threshold test/data/KLF4_f2.pat -p 0.001', &:read).strip.split("\t")
-    assert_equal '0.001', pvalue
-    assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
-  end
-  def test_process_default_pvalue
-    pvalue, threshold, real_pvalue = IO.popen('find_threshold test/data/KLF4_f2.pat', &:read).strip.split("\t")
-    assert_equal '0.0005', pvalue
-    assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold}"), real_pvalue
-  end
-  def test_custom_discretization
-    pvalue, threshold, real_pvalue = IO.popen('find_threshold test/data/KLF4_f2.pat -d 100',&:read).strip.split("\t")
-    assert_equal '0.0005', pvalue
-    assert_equal Helpers.obtain_pvalue_by_threshold("test/data/KLF4_f2.pat #{threshold} -d 100"), real_pvalue
-  end
-end
-
-class FindPvalueTest < Test::Unit::TestCase
-  def test_process_one_threshold
-    IO.popen('find_pvalue test/data/KLF4_f2.pat 4.1719'){|f|
-      assert_equal "4.1719\t1048.0\t0.00099945068359375\n", f.read
-    }
-  end
-  def test_process_several_thresholds
-    IO.popen('find_pvalue test/data/KLF4_f2.pat 4.1719 5.2403'){|f|
-      assert_equal "4.1719\t1048.0\t0.00099945068359375\n5.2403\t524.0\t0.000499725341796875\n", f.read
-    }
-  end
-  def test_process_several_thresholds_result_is_ordered
-    IO.popen('find_pvalue test/data/KLF4_f2.pat 5.2403 4.1719'){|f|
-      assert_equal "5.2403\t524.0\t0.000499725341796875\n4.1719\t1048.0\t0.00099945068359375\n", f.read
-    }
-  end
-  def test_custom_discretization
-    IO.popen('find_pvalue test/data/KLF4_f2.pat 5.2403 -d 100'){|f|
-      assert_equal "5.2403\t527.0\t0.0005025863647460938\n", f.read
-    }
-  end
-end
-
-
-class TestEvalSimilarity < Test::Unit::TestCase
-  def test_process_pair_of_pwms
-    IO.popen('eval_similarity test/data/KLF4_f2.pat test/data/SP1_f1.pat'){|f|
-      assert_equal "0.2420758234928527\n779.0\t11\n.>>>>>>>>>>\n>>>>>>>>>>>\n-1\tdirect\n", f.read
-    }
-  end
-  def test_process_another_pair_of_pwms
-    IO.popen('eval_similarity test/data/SP1_f1.pat test/data/AHR_si.pat'){|f|
-      assert_equal "0.0037332005973120955\n15.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>.\n1\tdirect\n", f.read
-    }
-  end
-  
-  def test_recognize_orientation_of_alignment
-    IO.popen('eval_similarity test/data/SP1_f1_revcomp.pat test/data/SP1_f1.pat'){|f|
-      assert_equal "1.0\n2033.0\t11\n>>>>>>>>>>>\n<<<<<<<<<<<\n0\trevcomp\n", f.read
-    }
-  end
-
-  def test_process_custom_discretization
-    IO.popen('eval_similarity test/data/SP1_f1.pat test/data/KLF4_f2.pat -d 1'){|f|
-      assert_equal "0.22754919499105544\n636.0\t11\n>>>>>>>>>>>\n.>>>>>>>>>>\n1\tdirect\n", f.read
-    }
-  end
-end
-
-class TestEvalAlignmentSimilarity < Test::Unit::TestCase
-  def test_process_at_optimal_alignment
-    IO.popen('eval_alignment test/data/KLF4_f2.pat test/data/SP1_f1.pat -1 direct '){|f|
-      assert_equal "0.2420758234928527\n779.0\t11\n.>>>>>>>>>>\n>>>>>>>>>>>\n-1\tdirect\n", f.read
-    }
-  end
-  def test_process_not_optimal_alignment
-    IO.popen('eval_alignment test/data/KLF4_f2.pat test/data/SP1_f1.pat 0 direct '){|f|
-      assert_equal "0.0017543859649122807\n7.0\t11\n>>>>>>>>>>.\n>>>>>>>>>>>\n0\tdirect\n", f.read
-    }
-  end
-  def test_process_at_optimal_alignment_reversed
-    IO.popen('eval_alignment test/data/KLF4_f2.pat test/data/SP1_f1.pat -1 revcomp '){|f|
-      assert_equal "0.0\n0.0\t11\n.>>>>>>>>>>\n<<<<<<<<<<<\n-1\trevcomp\n", f.read
-    }
-  end
-end
-
-class TestPreprocessCollection < Test::Unit::TestCase
-  def test_multipvalue_preproceessing
-    system('preprocess_collection ./test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
-    assert_equal File.read('test/data/test_collection.yaml'), File.read('test/data/test_collection.yaml.tmp')
-    File.delete 'test/data/test_collection.yaml.tmp'
-  end
-end
-
-class TestScanCollection < Test::Unit::TestCase
-  def test_scan_default_cutoff
-    assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt'), 
-                 IO.popen('scan_collection test/data/KLF4_f2.pat test/data/test_collection.yaml --silent', &:read)
-  end
-  def test_scan_and_output_all_results
-    assert_equal File.read('test/data/KLF4_f2_scan_results_all.txt'), 
-                 IO.popen('scan_collection test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent', &:read)
-      
-  end
-  def test_scan_precise_mode
-    assert_equal File.read('test/data/KLF4_f2_scan_results_precise_mode.txt'),
-                 IO.popen('scan_collection test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent', &:read)
-  end
-end