macroape 4.0.2 → 4.1.0

data/lib/macroape/cli/eval_similarity.rb

@@ -1,137 +1,138 @@
-require_relative '../../macroape'
-
-module Macroape
-  module CLI
-    module EvalSimilarity
-
-      def self.main(argv)
-        doc = <<-EOS.strip_doc
-        Command-line format:
-        #{run_tool_cmd} <1st matrix pat-file> <2nd matrix pat-file> [options]
-
-        Options:
-          [-p <P-value>]
-          [-d <discretization level>]
-          [--pcm] - treat the input file as Position Count Matrix. PCM-to-PWM transformation to be done internally.
-          [--boundary lower|upper] Upper boundary (default) means that the obtained P-value is greater than or equal to the requested P-value
-          [-b <background probabilities] ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25
-          [--first-threshold <threshold for the first matrix>]
-          [--second-threshold <threshold for the second matrix>]
-
-        Examples:
-          #{run_tool_cmd} motifs/KLF4_f2.pat motifs/SP1_f1.pat -p 0.0005 -d 100 -b 0.3,0.2,0.2,0.3
-        EOS
-
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          $stderr.puts doc
-          exit
-        end
-
-        pvalue = 0.0005
-        discretization = 10.0
-
-        first_background = [1,1,1,1]
-        second_background = [1,1,1,1]
-
-        max_hash_size = 10000000
-        max_pair_hash_size = 10000
-        pvalue_boundary = :upper
-
-        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
-        first_file = argv.shift
-        second_file = argv.shift
-        raise 'You should specify two input files' unless first_file and second_file
-
-        until argv.empty?
-          case argv.shift
-            when '-p'
-              pvalue = argv.shift.to_f
-            when '-d'
-              discretization = argv.shift.to_f
-            when '--max-hash-size'
-              max_hash_size = argv.shift.to_i
-            when '--max-2d-hash-size'
-              max_pair_hash_size = argv.shift.to_i
-            when '-b'
-              second_background = first_background = argv.shift.split(',').map(&:to_f)
-            when '-b1'
-              first_background = argv.shift.split(',').map(&:to_f)
-            when '-b2'
-              second_background = argv.shift.split(',').map(&:to_f)
-            when '--boundary'
-              pvalue_boundary = argv.shift.to_sym
-              raise 'boundary should be either lower or upper'  unless  pvalue_boundary == :lower || pvalue_boundary == :upper
-            when '--first-threshold'
-              predefined_threshold_first = argv.shift.to_f
-            when '--second-threshold'
-              predefined_threshold_second = argv.shift.to_f
-          end
-        end
-        raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless first_background == first_background.reverse
-        raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless second_background == second_background.reverse
-
-        if first_file == '.stdin' || second_file == '.stdin'
-          input = $stdin.read
-          parser = data_model.choose_parser(input).new(input)
-        end
-
-        if first_file == '.stdin'
-          input_first = parser.parse
-        else
-          raise "Error! File #{first_file} don't exist" unless File.exist?(first_file)
-          input_first = File.read(first_file)
-        end
-        pwm_first = data_model.new(input_first).set_parameters(background: first_background).to_pwm
-
-        if second_file == '.stdin'
-          input_second = parser.parse
-        else
-          raise "Error! File #{second_file} don't exist" unless File.exist?(second_file)
-          input_second = File.read(second_file)
-        end
-        pwm_second = data_model.new(input_second).set_parameters(background: second_background).to_pwm
-
-        pwm_first.set_parameters(background: first_background, max_hash_size: max_hash_size).discrete!(discretization)
-        pwm_second.set_parameters(background: second_background, max_hash_size: max_hash_size).discrete!(discretization)
-
-        cmp = Macroape::PWMCompare.new(pwm_first, pwm_second).set_parameters(max_pair_hash_size: max_pair_hash_size)
-
-        if predefined_threshold_first
-          threshold_first = predefined_threshold_first * discretization
-        else
-          if pvalue_boundary == :lower
-            threshold_first = pwm_first.threshold(pvalue)
-          else
-            threshold_first = pwm_first.weak_threshold(pvalue)
-          end
-        end
-
-        if predefined_threshold_second
-          threshold_second = predefined_threshold_second * discretization
-        else
-          if pvalue_boundary == :lower
-            threshold_second = pwm_second.threshold(pvalue)
-          else
-            threshold_second = pwm_second.weak_threshold(pvalue)
-          end
-        end
-
-        info = cmp.jaccard(threshold_first, threshold_second)
-        info.merge!(predefined_threshold_first: predefined_threshold_first,
-                    predefined_threshold_second: predefined_threshold_second,
-                    threshold_first: threshold_first.to_f / discretization,
-                    threshold_second: threshold_second.to_f / discretization,
-                    discretization: discretization,
-                    first_background: first_background,
-                    second_background: second_background,
-                    requested_pvalue: pvalue,
-                    pvalue_boundary: pvalue_boundary)
-        puts Helper.similarity_info_string(info)
-
-      rescue => err
-        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
-      end
-
-    end
-  end
-end
+require_relative '../../macroape'
+
+module Macroape
+  module CLI
+    module EvalSimilarity
+
+      def self.main(argv)
+        doc = <<-EOS.strip_doc
+        Command-line format:
+        #{run_tool_cmd} <1st matrix pat-file> <2nd matrix pat-file> [options]
+
+        Options:
+          [-p <P-value>]
+          [-d <discretization level>]
+          [--pcm] - treat the input file as Position Count Matrix. PCM-to-PWM transformation to be done internally.
+          [--boundary lower|upper] Upper boundary (default) means that the obtained P-value is greater than or equal to the requested P-value
+          [-b <background probabilities] ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25
+          [--first-threshold <threshold for the first matrix>]
+          [--second-threshold <threshold for the second matrix>]
+
+        Examples:
+          #{run_tool_cmd} motifs/KLF4_f2.pat motifs/SP1_f1.pat -p 0.0005 -d 100 -b 0.3,0.2,0.2,0.3
+        EOS
+
+        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          $stderr.puts doc
+          exit
+        end
+
+        pvalue = 0.0005
+        discretization = 10.0
+
+        first_background = Bioinform::Background::Wordwise
+        second_background = Bioinform::Background::Wordwise
+
+        max_hash_size = 10000000
+        max_pair_hash_size = 10000
+        pvalue_boundary = :upper
+
+        data_model = argv.delete('--pcm') ? :pcm : :pwm
+        first_file = argv.shift
+        second_file = argv.shift
+        raise 'You should specify two input files' unless first_file and second_file
+
+        until argv.empty?
+          case argv.shift
+            when '-p'
+              pvalue = argv.shift.to_f
+            when '-d'
+              discretization = argv.shift.to_f
+            when '--max-hash-size'
+              max_hash_size = argv.shift.to_i
+            when '--max-2d-hash-size'
+              max_pair_hash_size = argv.shift.to_i
+            when '-b'
+              second_background = first_background = Bioinform::Background.from_string(argv.shift)
+            when '-b1'
+              first_background = Bioinform::Background.from_string(argv.shift)
+            when '-b2'
+              second_background = Bioinform::Background.from_string(argv.shift)
+            when '--boundary'
+              pvalue_boundary = argv.shift.to_sym
+              raise 'boundary should be either lower or upper'  unless  pvalue_boundary == :lower || pvalue_boundary == :upper
+            when '--first-threshold'
+              predefined_threshold_first = argv.shift.to_f
+            when '--second-threshold'
+              predefined_threshold_second = argv.shift.to_f
+          end
+        end
+        raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless first_background.symmetric?
+        raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless second_background.symmetric?
+
+        raise "Error! File #{first_file} don't exist" unless File.exist?(first_file)
+        input_first = File.read(first_file)
+        input_first = Bioinform::MatrixParser.new.parse!(input_first)
+
+        raise "Error! File #{second_file} don't exist" unless File.exist?(second_file)
+        input_second = File.read(second_file)
+        input_second = Bioinform::MatrixParser.new.parse!(input_second)
+
+        case data_model
+        when :pcm
+          pcm_first = Bioinform::MotifModel::PCM.new(input_first[:matrix]).named(input_first[:name])
+          pwm_first = Bioinform::ConversionAlgorithms::PCM2PWMConverter.new(pseudocount: :log, background: first_background).convert(pcm_first)
+          pcm_second = Bioinform::MotifModel::PCM.new(input_second[:matrix]).named(input_second[:name])
+          pwm_second = Bioinform::ConversionAlgorithms::PCM2PWMConverter.new(pseudocount: :log, background: second_background).convert(pcm_second)
+        when :pwm
+          pwm_first = Bioinform::MotifModel::PWM.new(input_first[:matrix]).named(input_first[:name])
+          pwm_second = Bioinform::MotifModel::PWM.new(input_second[:matrix]).named(input_second[:name])
+        end
+
+        pwm_first = pwm_first.discreted(discretization)
+        pwm_second = pwm_second.discreted(discretization)
+
+        counting_first = PWMCounting.new(pwm_first, background: first_background, max_hash_size: max_hash_size)
+        counting_second = PWMCounting.new(pwm_second, background: second_background, max_hash_size: max_hash_size)
+
+        cmp = Macroape::PWMCompare.new(counting_first, counting_second).tap{|x| x.max_pair_hash_size = max_pair_hash_size }
+
+        if predefined_threshold_first
+          threshold_first = predefined_threshold_first * discretization
+        else
+          if pvalue_boundary == :lower
+            threshold_first = counting_first.threshold(pvalue)
+          else
+            threshold_first = counting_first.weak_threshold(pvalue)
+          end
+        end
+
+        if predefined_threshold_second
+          threshold_second = predefined_threshold_second * discretization
+        else
+          if pvalue_boundary == :lower
+            threshold_second = counting_second.threshold(pvalue)
+          else
+            threshold_second = counting_second.weak_threshold(pvalue)
+          end
+        end
+
+        info = cmp.jaccard(threshold_first, threshold_second)
+        info.merge!(predefined_threshold_first: predefined_threshold_first,
+                    predefined_threshold_second: predefined_threshold_second,
+                    threshold_first: threshold_first.to_f / discretization,
+                    threshold_second: threshold_second.to_f / discretization,
+                    discretization: discretization,
+                    first_background: first_background,
+                    second_background: second_background,
+                    requested_pvalue: pvalue,
+                    pvalue_boundary: pvalue_boundary)
+        puts Helper.similarity_info_string(info)
+
+      rescue => err
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+      end
+
+    end
+  end
+end

data/lib/macroape/cli/find_pvalue.rb

@@ -1,87 +1,93 @@
-require_relative '../../macroape'
-
-module Macroape
-  module CLI
-    module FindPValue
-
-      def self.main(argv)
-        doc = <<-EOS.strip_doc
-          Command-line format:
-          #{run_tool_cmd} <pat-file> <threshold list>... [options]
-
-          Options:
-            [-d <discretization level>]
-            [--pcm] - treat the input file as Position Count Matrix. PCM-to-PWM transformation to be done internally.
-            [-b <background probabilities] ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25
-
-          Examples:
-            #{run_tool_cmd} motifs/KLF4_f2.pat 7.32
-            #{run_tool_cmd} motifs/KLF4_f2.pat 7.32 4.31 5.42 -d 1000 -b 0.2,0.3,0.3,0.2
-        EOS
-
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          $stderr.puts doc
-          exit
-        end
-
-        discretization = 10000
-        background = [1,1,1,1]
-        thresholds = []
-        max_hash_size = 10000000
-
-        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
-        filename = argv.shift
-
-        loop do
-          begin
-            Float(argv.first)
-            thresholds << argv.shift.to_f
-          rescue
-            raise StopIteration
-          end
-        end
-
-        raise 'No input. You should specify input file' unless filename
-        raise 'You should specify at least one threshold' if thresholds.empty?
-
-        until argv.empty?
-          case argv.shift
-            when '-b'
-              background = argv.shift.split(',').map(&:to_f)
-            when '-d'
-              discretization = argv.shift.to_f
-            when '--max-hash-size'
-              max_hash_size = argv.shift.to_i
-          end
-        end
-
-
-        if filename == '.stdin'
-          input = $stdin.read
-        else
-          raise "Error! File #{filename} doesn't exist" unless File.exist?(filename)
-          input = File.read(filename)
-        end
-        pwm = data_model.new(input).set_parameters(background: background).to_pwm
-        pwm.set_parameters(background: background, max_hash_size: max_hash_size).discrete!(discretization)
-
-        counts = pwm.counts_by_thresholds(* thresholds.map{|count| count * discretization})
-        infos = []
-        thresholds.each do |threshold|
-          count = counts[threshold * discretization]
-          pvalue = count.to_f / pwm.vocabulary_volume
-          infos << {threshold: threshold,
-                    number_of_recognized_words: count,
-                    pvalue: pvalue}
-        end
-
-        puts Helper.find_pvalue_info_string( infos,
-                                            {discretization: discretization,
-                                            background: background} )
-      rescue => err
-        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
-      end
-
-    end
-  end
-end
+require_relative '../../macroape'
+
+module Macroape
+  module CLI
+    module FindPValue
+
+      def self.main(argv)
+        doc = <<-EOS.strip_doc
+          Command-line format:
+          #{run_tool_cmd} <pat-file> <threshold list>... [options]
+
+          Options:
+            [-d <discretization level>]
+            [--pcm] - treat the input file as Position Count Matrix. PCM-to-PWM transformation to be done internally.
+            [-b <background probabilities] ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25
+
+          Examples:
+            #{run_tool_cmd} motifs/KLF4_f2.pat 7.32
+            #{run_tool_cmd} motifs/KLF4_f2.pat 7.32 4.31 5.42 -d 1000 -b 0.2,0.3,0.3,0.2
+        EOS
+
+        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          $stderr.puts doc
+          exit
+        end
+
+        discretization = 10000
+        background = Bioinform::Background::Wordwise
+        thresholds = []
+        max_hash_size = 10000000
+
+        data_model = argv.delete('--pcm') ? :pcm : :pwm
+        filename = argv.shift
+
+        loop do
+          begin
+            Float(argv.first)
+            thresholds << argv.shift.to_f
+          rescue
+            raise StopIteration
+          end
+        end
+
+        raise 'No input. You should specify input file' unless filename
+        raise 'You should specify at least one threshold' if thresholds.empty?
+
+        until argv.empty?
+          case argv.shift
+            when '-b'
+              background = Bioinform::Background.from_string(argv.shift)
+            when '-d'
+              discretization = argv.shift.to_f
+            when '--max-hash-size'
+              max_hash_size = argv.shift.to_i
+          end
+        end
+
+        raise "Error! File #{filename} doesn't exist"  unless File.exist?(filename)
+        input = File.read(filename)
+
+        parser = Bioinform::MatrixParser.new
+        motif_data = parser.parse!(input)
+        case data_model
+        when :pcm
+          pcm = Bioinform::MotifModel::PCM.new(motif_data[:matrix]).named(motif_data[:name])
+          pwm = Bioinform::ConversionAlgorithms::PCM2PWMConverter.new(pseudocount: :log, background: background).convert(pcm)
+        when :pwm
+          pwm = Bioinform::MotifModel::PWM.new(motif_data[:matrix]).named(motif_data[:name])
+        end
+
+        pwm = pwm.discreted(discretization)
+        counting = PWMCounting.new(pwm, background: background, max_hash_size: max_hash_size)
+
+        counts = counting.counts_by_thresholds(* thresholds.map{|count| count * discretization})
+        infos = []
+        thresholds.each do |threshold|
+          count = counts[threshold * discretization]
+          pvalue = count.to_f / (counting.vocabulary_volume)
+          infos << {threshold: threshold,
+                    number_of_recognized_words: count,
+                    pvalue: pvalue}
+        end
+
+        puts Helper.find_pvalue_info_string(infos,
+                                            {discretization: discretization,
+                                            background: background} )
+      rescue => err
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+      end
+
+    end
+  end
+end