macroape 3.3.7 → 3.3.8

data/lib/macroape/cli/find_pvalue.rb

@@ -3,43 +3,31 @@ require_relative '../../macroape'
 module Macroape
   module CLI
     module FindPValue
-    
+
       def self.main(argv)
-        help_string = %q{
+        doc = <<-EOS.strip_doc
           Command-line format:
-          ruby find_pvalue.rb <pat-file> <threshold list> [options]
-                    or in linux
-          cat <pat-file> | ruby find_pvalue.rb .stdin <threshold> [options]
-            or on windows
-          type <pat-file> | ruby find_pvalue.rb .stdin <threshold> [options]
+          #{run_tool_cmd} <pat-file> <threshold list>... [options]
 
           Options:
             [-d <discretization level>]
-            [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]
-
-          Output format:
-            threshold_1 count_1  pvalue_1
-            threshold_2 count_2  pvalue_2
-            threshold_3 count_3  pvalue_3
-          The results are printed out in the same order as in the given threshold list.
+            [--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:
-            ruby find_pvalue.rb motifs/KLF4.pat 7.32 -d 1000 -b 0.2 0.3 0.2 0.3
-                     or on windows
-            type motifs/KLF4.pat | ruby find_pvalue.rb .stdin 7.32 4.31 5.42
-                     or in linux
-            cat motifs/KLF4.pat | ruby find_pvalue.rb .stdin 7.32 4.31 5.42
-        }
-      
-        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts help_string
+            #{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 = 1000000
+        max_hash_size = 10000000
 
         data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
         filename = argv.shift
@@ -53,21 +41,21 @@ module Macroape
           end
         end
 
-        raise "No input. You'd specify input source: filename or .stdin" unless filename
+        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(4).map(&:to_f)
+              background = argv.shift.split(',').map(&:to_f)
             when '-d'
               discretization = argv.shift.to_f
-            when '-m'
+            when '--max-hash-size'
               max_hash_size = argv.shift.to_i
           end
         end
 
-        
+
         if filename == '.stdin'
           input = $stdin.read
         else
@@ -78,14 +66,22 @@ module Macroape
         pwm.set_parameters(background: background, max_hash_size: max_hash_size).discrete!(discretization)
 
         counts = pwm.counts_by_thresholds(* thresholds.map{|count| count * discretization})
-        pvalues = counts.map{|count| count.to_f / pwm.vocabulary_volume}
-        pvalues.zip(thresholds,counts).each{|pvalue,threshold,count|
-          puts "#{threshold}\t#{count}\t#{pvalue}"
-        }
+        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"
+        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_threshold.rb

@@ -3,65 +3,64 @@ require_relative '../../macroape'
 module Macroape
   module CLI
     module FindThreshold
-    
+
       def self.main(argv)
-        help_string = %q{
-          Command-line format::
-          ruby find_threshold.rb <pat-file> [options]
-                    or in linux
-          cat <pat-file> | ruby find_threshold.rb .stdin [options]
-                      or on windows
-          type <pat-file> | ruby find_threshold.rb .stdin [options]
+        doc = <<-EOS.strip_doc
+          Command-line format:
+          #{run_tool_cmd} <pat-file> [<list of P-values>...] [options]
 
           Options:
-            [-p <list of P-values>]
             [-d <discretization level>]
-            [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]
-
-          Output format:
-            requested_pvalue_1 threshold_1 achieved_pvalue_1
-            requested_pvalue_2 threshold_2 achieved_pvalue_2
-
+            [--pcm] - treat the input file as Position Count Matrix. PCM-to-PWM transformation to be done internally.
+            [--boundary lower|upper] Lower boundary (default) means that the obtained P-value is less 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
 
           Example:
-            ruby find_threshold.rb motifs/KLF4.pat -p 0.001 0.0001 0.0005 -d 1000 -b 0.4 0.3 0.2 0.1
-        }
-      
-        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts help_string
+            #{run_tool_cmd} motifs/KLF4_f2.pat
+            #{run_tool_cmd} motifs/KLF4_f2.pat 0.001 0.0001 0.0005 -d 1000 -b 0.4,0.3,0.2,0.1
+        EOS
+
+        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          STDERR.puts doc
           exit
         end
-        
+
         background = [1,1,1,1]
         default_pvalues = [0.0005]
         discretization = 10000
-        max_hash_size = 1000000
-        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM      
+        max_hash_size = 10000000
+        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
+
+        pvalue_boundary = :lower
+
 
         filename = argv.shift
-        raise "No input. You'd specify input source: filename or .stdin" unless filename
+        raise 'No input. You should specify input file' unless filename
 
         pvalues = []
+        loop do
+          begin
+            Float(argv.first)
+            pvalues << argv.shift.to_f
+          rescue
+            raise StopIteration
+          end
+        end
+        pvalues = default_pvalues if pvalues.empty?
+
         until argv.empty?
           case argv.shift
             when '-b'
-              background = argv.shift(4).map(&:to_f)
-            when '-m'
+              background = argv.shift.split(',').map(&:to_f)
+            when '--max-hash-size'
               max_hash_size = argv.shift.to_i
-            when '-p'
-              loop do
-                begin
-                  Float(argv.first)
-                  pvalues << argv.shift.to_f
-                rescue
-                  raise StopIteration
-                end
-              end
             when '-d'
               discretization = argv.shift.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
             end
         end
-        pvalues = default_pvalues if pvalues.empty?
 
         if filename == '.stdin'
           input = $stdin.read
@@ -72,14 +71,26 @@ module Macroape
         pwm = data_model.new(input).to_pwm
         pwm.set_parameters(background: background, max_hash_size: max_hash_size).discrete!(discretization)
 
-        pwm.thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
-          puts "#{pvalue}\t#{threshold / discretization}\t#{real_pvalue}"
+        infos = []
+        collect_infos_proc = ->(pvalue, threshold, real_pvalue) do
+          infos << {expected_pvalue: pvalue,
+                    threshold: threshold / discretization,
+                    real_pvalue: real_pvalue,
+                    recognized_words: pwm.vocabulary_volume * real_pvalue }
         end
-        
+        if pvalue_boundary == :lower
+          pwm.thresholds(*pvalues, &collect_infos_proc)
+        else
+          pwm.weak_thresholds(*pvalues, &collect_infos_proc)
+        end
+        puts Helper.threshold_infos_string(infos,
+                                          {discretization: discretization,
+                                          background: background,
+                                          pvalue_boundary: pvalue_boundary} )
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
+        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/preprocess_collection.rb

@@ -5,87 +5,76 @@ require 'shellwords'
 module Macroape
   module CLI
     module PreprocessCollection
-    
+
       def self.main(argv)
-        help_string = %q{
-        Command-line format:
-          ruby preprocess_collection.rb <file or folder with PWMs or .stdin with filenames> [options]
-
-        Options:
-          [-p <list of P-values>]
-          [-d <rough discretization> <precise discretization>]
-          [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]
-          [-o <output file>]
-          [-n <name>] - specify name for a collection. Default filename is based on this parameter
-          [--silent] - don't show current progress information during scan (by default this information's written into stderr)
-          [--pcm] - treats your input motifs as PCM-s. Motifs are converted to PWMs internally so output is the same as for according PWMs
-
-        The tool stores preprocessed Macroape collection to the specified YAML-file.
-
-        Example:
-          ruby preprocess_collection.rb ./motifs -p 0.001 0.0005 0.0001 -d 1 10 -b 0.2 0.3 0.2 0.3 -o collection.yaml
-        }
-
-        if ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts help_string
+        doc = <<-EOS.strip_doc
+          Command-line format:
+          #{run_tool_cmd} <file or folder with PWMs or .stdin with filenames> <output file> [options]
+
+          Options:
+            [-p <list of P-values>] - comma separated(no spaces allowed) list of P-values to precalculate thresholds
+            [-d <rough discretization>,<precise discretization>] - set discretization rates, comma delimited (no spaces allowed), order doesn't matter
+            [--silent] - hide current progress information during scan (printed to stderr by default)
+            [--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
+
+          The tool preprocesses and stores Macroape motif collection in the specified YAML-file.
+
+          Example:
+            #{run_tool_cmd} ./motifs  collection.yaml -p 0.001,0.0005,0.0001 -d 1,10 -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
 
         data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
-        
+
         default_pvalues = [0.0005]
         background = [1,1,1,1]
         rough_discretization = 1
         precise_discretization = 10
-        output_file = 'collection.yaml'
-        max_hash_size = 1000000
-        
+        max_hash_size = 10000000
+
         data_source = argv.shift
-        
-        raise "No input. You'd specify file or folder with pwms" unless data_source
+        output_file = argv.shift
+
+        raise 'No input. You should specify file or folder with pwms' unless data_source
         raise "Error! File or folder #{data_source} doesn't exist" unless Dir.exist?(data_source) || File.exist?(data_source) || data_source == '.stdin'
+        raise 'You should specify output file'  unless output_file
 
         pvalues = []
         silent = false
-        output_file_specified = false
+        pvalue_boundary = :upper
+
         until argv.empty?
           case argv.shift
             when '-b'
-              background = argv.shift(4).map(&:to_f)
+              background = argv.shift.split(',').map(&:to_f)
               raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless background == background.reverse
             when '-p'
-              loop do
-                begin
-                  Float(argv.first)
-                  pvalues << argv.shift.to_f
-                rescue
-                  raise StopIteration
-                end
-              end
+              pvalues = argv.shift.split(',').map(&:to_f)
             when '-d'
-              rough_discretization, precise_discretization = argv.shift(2).map(&:to_f).sort
-            when '-o'
-              output_file = argv.shift
-              output_file_specified = true
-            when '-m'
+              rough_discretization, precise_discretization = argv.shift.split(',').map(&:to_f).sort
+            when '--max-hash-size'
               max_hash_size = argv.shift.to_i
-            when '-n'
-              collection_name = argv.shift
             when '--silent'
               silent = true
+            when '--boundary'
+              pvalue_boundary = argv.shift.to_sym
+              raise 'boundary should be either lower or upper'  unless  pvalue_boundary == :lower || pvalue_boundary == :upper
             end
         end
         pvalues = default_pvalues  if pvalues.empty?
 
-        collection = Bioinform::Collection.new(rough_discretization: rough_discretization, 
+        collection = Bioinform::Collection.new(rough_discretization: rough_discretization,
                                 precise_discretization: precise_discretization,
                                 background: background,
                                 pvalues: pvalues)
-        if collection_name
-          collection.name = collection_name
-          output_file = "#{collection_name}.yaml"  if !output_file_specified
-        end
-        
+
+        data_source = data_source.gsub("\\",'/')
         if File.directory?(data_source)
           motifs = Dir.glob(File.join(data_source,'*')).sort.map do |filename|
             pwm = data_model.new(File.read(filename))
@@ -106,12 +95,12 @@ module Macroape
         else
           raise "Specified data source `#{data_source}` is neither directory nor file nor even .stdin"
         end
-        
+
         pwms = motifs.map(&:to_pwm)
-        
+
         pwms.each_with_index do |pwm,index|
-          STDERR.puts "#{index + 1} -- Name: #{pwm.name}, Length: #{pwm.length}"  unless silent
-          
+          STDERR.puts "Motif #{pwm.name}, length: #{pwm.length} (#{index+1} of #{pwms.size}, #{index*100/pwms.size}% complete)"  unless silent
+
           # When support of onefile collections is introduced - then here should be check if name exists.
           # Otherwise it should skip motif and tell you about this
           # Also two command line options to fail on skipping or to skip silently should be included
@@ -120,7 +109,8 @@ module Macroape
           pwm.set_parameters(background: background, max_hash_size: max_hash_size)
           skip_motif = false
 
-          pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
+
+          fill_rough_infos = ->(pvalue, threshold, real_pvalue) do
             if real_pvalue == 0
               $stderr.puts "#{pwm.name} at pvalue #{pvalue} has threshold that yields real-pvalue 0 in rough mode. Rough calculation will be skipped"
             else
@@ -128,7 +118,7 @@ module Macroape
             end
           end
 
-          pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
+          fill_precise_infos = ->(pvalue, threshold, real_pvalue) do
             if real_pvalue == 0
               $stderr.puts "#{pwm.name} at pvalue #{pvalue} has threshold that yields real-pvalue 0 in precise mode. Motif will be excluded from collection"
               skip_motif = true
@@ -136,13 +126,33 @@ module Macroape
               info.precise[pvalue] = threshold / precise_discretization
             end
           end
+
+          if pvalue_boundary == :lower
+            pwm.discrete(rough_discretization).thresholds(*pvalues, &fill_rough_infos)
+          else
+            pwm.discrete(rough_discretization).weak_thresholds(*pvalues, &fill_rough_infos)
+          end
+
+          if pvalue_boundary == :lower
+            pwm.discrete(precise_discretization).thresholds(*pvalues, &fill_precise_infos)
+          else
+            pwm.discrete(precise_discretization).weak_thresholds(*pvalues,&fill_precise_infos)
+          end
           collection.add_pm(pwm, info)  unless skip_motif
         end
+        STDERR.puts "100% complete. Saving results"  unless silent
         File.open(output_file, 'w') do |f|
           f.puts(collection.to_yaml)
         end
+        puts OutputInformation.new{|infos|
+          infos.add_parameter('P', 'P-value list', pvalues.join(','))
+          infos.add_parameter('VR', 'discretization value, rough', rough_discretization)
+          infos.add_parameter('VP', 'discretization value, precise', precise_discretization)
+          infos.add_parameter('PB', 'P-value boundary', pvalue_boundary)
+          infos.background_parameter('B', 'background', background)
+        }.result
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
+        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end