macroape 3.3.3 → 3.3.4

data/lib/macroape/cli/preprocess_collection.rb

@@ -0,0 +1,123 @@
+require 'macroape'
+require 'yaml'
+
+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 PWMs> [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>]
+          [--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 argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          STDERR.puts help_string
+          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
+        
+        data_source = argv.shift
+        
+        raise "No input. You'd 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'
+
+        pvalues = []
+        silent = false
+        until argv.empty?
+          case argv.shift
+            when '-b'
+              background = argv.shift(4).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
+            when '-d'
+              rough_discretization, precise_discretization = argv.shift(2).map(&:to_f).sort
+            when '-o'
+              output_file = argv.shift
+            when '-m'
+              max_hash_size = argv.shift.to_i
+            when '--silent'
+              silent = true
+            end
+        end
+        pvalues = default_pvalues  if pvalues.empty?
+
+        collection = Macroape::Collection.new(rough_discretization, precise_discretization, background, pvalues)
+        
+        if File.directory?(data_source)
+            motifs = Dir.glob(File.join(data_source,'*')).map do |filename|
+            pwm = data_model.new(File.read(filename))
+            pwm.name ||= File.basename(filename, File.extname(filename))
+            pwm
+          end
+        elsif File.file?(data_source)
+          input = File.read(data_source)
+          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
+        elsif data_source == '.stdin'
+          input = $stdin.read
+          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
+        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
+          
+          # 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
+
+          info = {rough: {}, precise: {}}
+          pwm.background!(background).max_hash_size!(max_hash_size)
+
+          pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
+            info[:rough][pvalue] = threshold / rough_discretization
+          end
+
+          pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
+            info[:precise][pvalue] = threshold / precise_discretization
+          end
+
+          collection.add_pwm(pwm, info)
+        end
+        File.open(output_file,'w') do |f|
+          f.puts(collection.to_yaml)
+        end
+      rescue => err
+        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
+      end
+
+    end
+  end
+end

data/lib/macroape/cli/scan_collection.rb

@@ -0,0 +1,141 @@
+require 'macroape'
+require 'yaml'
+
+module Macroape
+  module CLI
+    module ScanCollection
+    
+      def self.main(argv)
+        help_string = %q{
+        Command-line format:
+        ruby scan_collection.rb <pat-file> <collection> [options]
+                or in linux
+        cat <pat-file> | ruby scan_collection.rb .stdin <collection> [options]
+                or on windows
+        type <pat-file> | ruby scan_collection.rb .stdin <collection> [options]
+
+        Options:
+          [-p <P-value>]
+          [-c <similarity cutoff (minimal similarity to be included in output)> ] or [--all], '-c 0.05' by default
+          [--precise [<level, minimal similarity to check on a more precise discretization level on the second pass>]], off by default, '--precise 0.01' if level is not set
+          [--silent] - don't show current progress information during scan (by default this information's written into stderr)
+
+        Output format:
+         <name> <similarity jaccard index> <shift> <overlap> <orientation> * [in case that result calculated on the second pass(in precise mode)]
+            Attention! Name can contain whitespace characters.
+            Attention! The shift and orientation are reported for the collection matrix relative to the query matrix.
+
+        Example:
+          ruby scan_collection.rb motifs/KLF4.pat collection.yaml -p 0.005
+                    or in linux
+          cat motifs/KLF4.pat | ruby scan_collection.rb .stdin collection.yaml -p 0.005 --precise 0.03
+        }
+
+        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          STDERR.puts help_string
+          exit
+        end
+
+        filename = argv.shift
+        collection_file = argv.shift
+        raise "No input. You'd specify input source for pat: filename or .stdin" unless filename
+        raise "No input. You'd specify input file with collection" unless collection_file
+        raise "Collection file #{collection_file} doesn't exist" unless File.exist?(collection_file)
+
+        pvalue = 0.0005
+        cutoff = 0.05 # minimal similarity to output
+        collection = YAML.load_file(collection_file)
+        background_query = collection.background
+        max_hash_size = 1000000
+        max_pair_hash_size = 1000
+        
+        silent = false
+        precision_mode = :rough
+        until argv.empty?
+          case argv.shift
+            when '-bq'
+              background_query = argv.shift(4).map(&:to_f)
+              raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless background_query == background_query.reverse
+            when '-p'
+              pvalue = argv.shift.to_f
+            when '-m'
+              max_hash_size = argv.shift.to_i        
+            when '-md'
+              max_pair_hash_size = argv.shift.to_i
+            when '-c'
+              cutoff = argv.shift.to_f
+            when '--all'
+              cutoff = 0.0
+            when '--silent'
+              silent = true
+            when '--precise'
+              precision_mode = :precise
+              begin
+                Float(argv.first)
+                minimal_similarity = argv.shift.to_f
+              rescue
+                minimal_similarity = 0.05
+              end
+          end
+        end
+
+        raise "Thresholds for pvalue #{pvalue} aren't presented in collection (#{collection.pvalues.join(', ')}). Use one of listed pvalues or recalculate the collection with needed pvalue" unless collection.pvalues.include? pvalue
+        
+        if filename == '.stdin'
+          query_pwm = Bioinform::PWM.new( $stdin.read )
+        else
+          raise "Error! File #{filename} doesn't exist" unless File.exist?(filename)
+          query_pwm = Bioinform::PWM.new(File.read(filename))
+        end
+
+        query_pwm.background(background_query).max_hash_size(max_hash_size)
+        
+        query_pwm_rough = query_pwm.discrete(collection.rough_discretization)
+        query_pwm_precise = query_pwm.discrete(collection.precise_discretization)
+
+        query_threshold_rough = query_pwm_rough.threshold(pvalue)
+        query_threshold_precise = query_pwm_precise.threshold(pvalue)
+
+        similarities = {}
+        precision_file_mode = {}
+
+        collection.pwms.each_key do |name|
+          pwm = collection.pwms[name]
+          pwm.background(collection.background).max_hash_size(max_hash_size)
+          pwm_rough = pwm.discrete(collection.rough_discretization)
+          pwm_precise = pwm.discrete(collection.precise_discretization)
+          
+          pwm_info = collection.infos[name]
+          
+          pwm_threshold_rough = pwm_info[:rough][pvalue] * collection.rough_discretization
+          pwm_threshold_precise = pwm_info[:precise][pvalue] * collection.precise_discretization
+          
+          
+          STDERR.puts pwm.name unless silent
+          cmp = Macroape::PWMCompare.new(query_pwm_rough, pwm_rough).max_hash_size(max_pair_hash_size)
+          info = cmp.jaccard(query_threshold_rough, pwm_threshold_rough)
+          precision_file_mode[name] = :rough
+
+          if precision_mode == :precise and info[:similarity] >= minimal_similarity
+            cmp = Macroape::PWMCompare.new(query_pwm_precise, pwm_precise).max_hash_size(max_pair_hash_size)
+            info = cmp.jaccard(query_threshold_precise, pwm_threshold_precise)
+            precision_file_mode[name] = :precise
+          end
+          similarities[name] = info
+        end
+
+        puts "#pwm\tsimilarity\tshift\toverlap\torientation"
+        similarities.sort_by do |name, info|
+          info[:similarity]
+        end.reverse.each do |name, info|
+          precision_text = (precision_file_mode[name] == :precise) ? "\t*" : ""
+          puts "#{name}\t#{info[:similarity]}\t#{info[:shift]}\t#{info[:overlap]}\t#{info[:orientation]}#{precision_text}" if info[:similarity] >= cutoff
+        end
+
+      rescue => err
+        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
+      end
+      
+    end
+  end
+end

data/lib/macroape/cli.rb

@@ -0,0 +1,5 @@
+module Macroape
+  module CLI
+    
+  end
+end

data/lib/macroape/counting.rb

@@ -1,5 +1,19 @@
 module Bioinform
   class PWM
+    # sets or gets limit size of calculation hash. It's a defence against overuse CPU resources by non-appropriate data
+    def max_hash_size!(new_max_hash_size)
+      @max_hash_size = new_max_hash_size
+      self
+    end
+    
+    def max_hash_size(*args)
+      case args.size
+      when 0 then @max_hash_size
+      when 1 then max_hash_size!(args.first)
+      else raise ArgumentError, '#max_hash_size method can get 0 or 1 argument'
+      end
+    end
+    
     def threshold(pvalue)
       thresholds(pvalue){|_, thresh, _| return thresh }
     end
@@ -51,7 +65,7 @@ module Bioinform
       scores = { 0 => 1 }
       length.times do |column|
         scores.replace recalc_score_hash(scores, @matrix[column], threshold - best_suffix(column + 1))
-        raise 'Hash overflow in PWM::ThresholdByPvalue#count_distribution_after_threshold' if defined? MaxHashSizeSingle and scores.size > MaxHashSizeSingle
+        raise 'Hash overflow in PWM::ThresholdByPvalue#count_distribution_after_threshold'  if max_hash_size && scores.size > max_hash_size
       end
       scores
     end

data/lib/macroape/pwm_compare.rb

@@ -1,5 +1,19 @@
 module Macroape
   class PWMCompare
+    # sets or gets limit of summary size of calculation hash. It's a defence against overuse CPU resources by non-appropriate data
+    def max_hash_size!(new_max_hash_size)
+      @max_hash_size = new_max_hash_size
+      self
+    end
+    
+    def max_hash_size(*args)
+      case args.size
+      when 0 then @max_hash_size
+      when 1 then max_hash_size!(args.first)
+      else raise ArgumentError, '#max_hash_size method can get 0 or 1 argument'
+      end
+    end
+  
     attr_reader :first, :second
     def initialize(first, second)
       @first = first
@@ -11,10 +25,16 @@ module Macroape
         alignment.alignment_infos.merge( alignment.jaccard(threshold_first, threshold_second) )
       end.max_by {|alignment_infos| alignment_infos[:similarity] }
     end
+    
+    def jaccard_by_pvalue(pvalue)
+      threshold_first = first.threshold(pvalue)
+      threshold_second = second.threshold(pvalue)
+      jaccard(threshold_first, threshold_second)
+    end
 
     def each_alignment
       (-second.length..first.length).to_a.product([:direct,:revcomp]) do |shift, orientation|
-        yield PWMCompareAligned.new(first, second, shift, orientation)
+        yield PWMCompareAligned.new(first, second, shift, orientation).max_hash_size(max_hash_size)
       end
     end
 

data/lib/macroape/pwm_compare_aligned.rb

@@ -117,6 +117,12 @@ module Macroape
       { similarity: similarity,  tanimoto: 1.0 - similarity,  recognized_by_both: intersect,
         recognized_by_first: f,  recognized_by_second: s }
     end
+    
+    def jaccard_by_pvalue(pvalue)
+      threshold_first = first.threshold(pvalue)
+      threshold_second = second.threshold(pvalue)
+      jaccard(threshold_first, threshold_second)
+    end
 
     def self.calculate_alignment_length(first_len, second_len, shift)
       if shift > 0
@@ -125,6 +131,21 @@ module Macroape
         [first_len - shift, second_len].max
       end
     end
+    
+    # sets or gets limit of summary size of calculation hash. It's a defence against overuse CPU resources by non-appropriate data
+    def max_hash_size!(new_max_hash_size)
+      @max_hash_size = new_max_hash_size
+      self
+    end
+    
+    def max_hash_size(*args)
+      case args.size
+      when 0 then @max_hash_size
+      when 1 then max_hash_size!(args.first)
+      else raise ArgumentError, '#max_hash_size method can get 0 or 1 argument'
+      end
+    end
+    
 
   end
 

data/lib/macroape/version.rb

@@ -1,3 +1,3 @@
 module Macroape
-  VERSION = "3.3.3"
+  VERSION = "3.3.4"
 end

data/macroape.gemspec

@@ -15,5 +15,5 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
   gem.version       = Macroape::VERSION
   
-  gem.add_dependency('bioinform', '>= 0.1.2')
+  gem.add_dependency('bioinform', '>= 0.1.5')
 end

data/test/align_motifs_test.rb

@@ -0,0 +1,12 @@
+require 'test_helper'
+
+class TestAlignmotifs < Test::Unit::TestCase
+  def test_align_motifs
+    assert_equal "test/data/KLF4_f2.pat\t0\tdirect\ntest/data/KLF3_f1.pat\t-4\tdirect\ntest/data/SP1_f1_revcomp.pat\t-1\trevcomp\n", 
+      Helpers.align_motifs_output('test/data/KLF4_f2.pat  test/data/KLF3_f1.pat  test/data/SP1_f1_revcomp.pat')
+  end
+  def test_align_pcm_motifs
+    assert_equal "test/data/KLF4_f2.pcm\t0\tdirect\ntest/data/KLF3_f1.pcm\t-4\tdirect\ntest/data/SP1_f1_revcomp.pcm\t-1\trevcomp\n", 
+      Helpers.align_motifs_output('--pcm test/data/KLF4_f2.pcm  test/data/KLF3_f1.pcm  test/data/SP1_f1_revcomp.pcm')
+  end
+end

data/test/data/KLF3_f1.pat

@@ -0,0 +1,16 @@
+KLF3_f1
+0.22156599923632986 0.0484147821994171 -1.5783984904108685 0.4028344703516524 
+0.3691145643098263 -0.42654798884705847 0.5273776327056031 -1.5783984904108685 
+-1.5783984904108685 1.006572764992778 -0.5055850184352592 -0.7889208019368309 
+-0.42654798884705847 0.3691145643098263 -0.5055850184352592 0.26054379103002956 
+0.26054379103002956 -1.5783984904108685 -0.5055850184352592 0.6381135377904803 
+-0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685 
+-1.5783984904108685 -1.5783984904108685 1.0765817190154965 -0.42654798884705847 
+-1.5783984904108685 -1.5783984904108685 1.2181964566417396 -1.5783984904108685 
+-1.5783984904108685 -1.5783984904108685 -1.5783984904108685 1.2181964566417396 
+-0.42654798884705847 -1.5783984904108685 1.0765817190154965 -1.5783984904108685 
+-1.5783984904108685 -1.5783984904108685 0.3691145643098263 0.7612432224843741 
+-0.42654798884705847 0.0484147821994171 0.7378003724947412 -1.5783984904108685 
+-1.5783984904108685 -0.5055850184352592 0.9312911055808129 -0.42654798884705847 
+-0.1611290354980871 0.611557817476478 -0.42654798884705847 -0.42654798884705847 
+-0.03791418689319392 -1.1459600292730023 -1.1459600292730023 0.8760382926050381 

data/test/data/KLF3_f1.pcm

@@ -0,0 +1,16 @@
+KLF3_f1
+2.625  2.125  0.0  3.25
+3.125  1.125  3.75  0.0
+0.0  6.375  1.0  0.625
+1.125  3.125  1.0  2.75
+2.75  0.0  1.0  4.25
+1.125  0.0  6.875  0.0
+0.0  0.0  6.875  1.125
+0.0  0.0  8.0  0.0
+0.0  0.0  0.0  8.0
+1.125  0.0  6.875  0.0
+0.0  0.0  3.125  4.875
+1.125  2.125  4.75  0.0
+0.0  1.0  5.875  1.125
+1.625  4.125  1.125  1.125
+1.90625  0.28125  0.28125  5.53125

data/test/data/KLF4_f2.pcm

@@ -0,0 +1,11 @@
+KLF4_f2
+1233.46088405354  93.18173277811673  1036.6014857092885  1258.2948629970272
+263.979242343185  5.314520555872139  3347.5949971525274  4.650205486388122
+76.7700780003465  6.643150694840173  3529.4896409394937  8.636095903292224
+57.86097393406657  18.102585643439472  3520.3342027139347  25.24120324653207
+518.1947904009378  1545.9062946905135  22.396758181071043  1535.0411222654507
+137.98151691820345  9.300410972776241  3456.320530770924  17.936506876068467
+115.27647661640499  81.51802997128804  1861.9425868567278  1562.801872093553
+227.8095486111286  42.84555258785854  3278.6396005325996  72.244263806387
+108.73384179997886  134.47328134862394  3162.880454846513  215.45138754285665
+238.49636899561344  2225.9561104691043  402.40727964384774  754.6792064294074

data/test/data/SP1_f1.pat

@@ -1,12 +1,12 @@
 > SP1_f1
--0.24435707885585334  -0.6748234046937317  0.8657012535789861  -1.1060188862599292
--1.0631255752097801  -2.1119259694238686  1.0960627561110399  -0.6138563775211981
--0.387227623476054  -2.973985191321805  1.1807800242010371  -4.338927525031567
--4.563896055436894  -2.916163300253228  1.3684371349982631  -5.077972423609655
--2.2369752892820087  -3.719643631330185  1.3510439136452728  -4.8899306705082335
--0.07473964149330914  0.9449196547620103  -2.624685764808605  -0.851098348782244
--1.9643526491643326  -2.9784027708801153  1.3113096718240569  -2.3243342594990253
--4.015548413965584  -3.138426807809667  1.338748858978805  -2.0846739035376483
--0.4450938582835542  -2.2510053061629707  1.126543157436868  -1.7780413702431377
--1.1896356092245055  -1.2251832285630033  1.163676006374752  -1.6080243648157357
--0.5166047365590577  0.7641033353626651  -0.28626775700282125  -0.6825482097865606
+-0.24435707885585292	-0.674823404693731	0.8657012535789866	-1.1060188862599287
+-1.0631255752097797	-2.111925969423868	1.0960627561110403	-0.6138563775211977
+-0.3872276234760535	-2.9739851913218045	1.1807800242010378	-4.338927525031566
+-4.563896055436894	-2.9161633002532277	1.3684371349982638	-5.077972423609655
+-2.2369752892820083	-3.7196436313301846	1.3510439136452734	-4.889930670508233
+-0.07473964149330865	0.944919654762011	-2.6246857648086044	-0.8510983487822436
+-1.9643526491643322	-2.978402770880115	1.3113096718240573	-2.324334259499025
+-4.0155484139655835	-3.1384268078096667	1.3387488589788057	-2.084673903537648
+-0.44509385828355363	-2.2510053061629702	1.1265431574368685	-1.7780413702431372
+-1.1896356092245048	-1.2251832285630027	1.1636760063747527	-1.6080243648157353
+-0.5166047365590571	0.7641033353626657	-0.2862677570028208	-0.68254820978656

data/test/data/SP1_f1.pcm

@@ -0,0 +1,12 @@
+SP1_f1
+682.6436366358055  443.1455214015781  2075.655346294993  287.211468117951
+299.8883246804867  103.74338315843572  2613.8927022405364  471.1315623708902
+591.4892493324709  42.631827541794564  2845.1654083148564  9.36948726124641
+7.071084742361592  45.29093411231232  3432.8847704374107  3.409183158303573
+91.308984085713  19.1536481364332  3373.656949880137  4.5363903481026
+809.2082973387932  2246.941954176211  61.30766021687515  371.19806071846244
+120.56476435866055  42.4349244403591  3242.1560628684038  83.50022078295852
+13.72524477409959  35.858220519297525  3332.4066864946167  106.66582066236779
+558.1188080161639  90.0084504200356  2694.854973210736  145.67374080342415
+264.0088462230318  254.7175868081866  2796.88087480315  173.0486646159857
+519.46013914282  1874.9349086474765  654.5411208373813  439.7198038226514

data/test/data/SP1_f1_revcomp.pat

@@ -1,12 +1,12 @@
 SP1_f1_revcomp
--0.6825482097865606 -0.28626775700282125 0.7641033353626651 -0.5166047365590577
--1.6080243648157357 1.163676006374752 -1.2251832285630033 -1.1896356092245055
--1.7780413702431377 1.126543157436868 -2.2510053061629707 -0.4450938582835542
--2.0846739035376483 1.338748858978805 -3.138426807809667 -4.015548413965584
--2.3243342594990253 1.3113096718240569 -2.9784027708801153 -1.9643526491643326
--0.851098348782244 -2.624685764808605 0.9449196547620103 -0.07473964149330914
--4.8899306705082335 1.3510439136452728 -3.719643631330185 -2.2369752892820087
--5.077972423609655 1.3684371349982631 -2.916163300253228 -4.563896055436894
--4.338927525031567 1.1807800242010371 -2.973985191321805 -0.387227623476054
--0.6138563775211981 1.0960627561110399 -2.1119259694238686 -1.0631255752097801
--1.1060188862599292 0.8657012535789861 -0.6748234046937317 -0.24435707885585334
+-0.68254820978656	-0.2862677570028208	0.7641033353626657	-0.5166047365590571
+-1.6080243648157353	1.1636760063747527	-1.2251832285630027	-1.1896356092245048
+-1.7780413702431372	1.1265431574368685	-2.2510053061629702	-0.44509385828355363
+-2.084673903537648	1.3387488589788057	-3.1384268078096667	-4.0155484139655835
+-2.324334259499025	1.3113096718240573	-2.978402770880115	-1.9643526491643322
+-0.8510983487822436	-2.6246857648086044	0.944919654762011	-0.07473964149330865
+-4.889930670508233	1.3510439136452734	-3.7196436313301846	-2.2369752892820083
+-5.077972423609655	1.3684371349982638	-2.9161633002532277	-4.563896055436894
+-4.338927525031566	1.1807800242010378	-2.9739851913218045	-0.3872276234760535
+-0.6138563775211977	1.0960627561110403	-2.111925969423868	-1.0631255752097797
+-1.1060188862599287	0.8657012535789866	-0.674823404693731	-0.24435707885585292

data/test/data/SP1_f1_revcomp.pcm

@@ -0,0 +1,12 @@
+SP1_f1
+439.7198038226514  654.5411208373813  1874.9349086474765  519.46013914282
+173.0486646159857  2796.88087480315  254.7175868081866  264.0088462230318
+145.67374080342415  2694.854973210736  90.0084504200356  558.1188080161639
+106.66582066236779  3332.4066864946167  35.858220519297525  13.72524477409959
+83.50022078295852  3242.1560628684038  42.4349244403591  120.56476435866055
+371.19806071846244  61.30766021687515  2246.941954176211  809.2082973387932
+4.5363903481026  3373.656949880137  19.1536481364332  91.308984085713
+3.409183158303573  3432.8847704374107  45.29093411231232  7.071084742361592
+9.36948726124641  2845.1654083148564  42.631827541794564  591.4892493324709
+471.1315623708902  2613.8927022405364  103.74338315843572  299.8883246804867
+287.211468117951  2075.655346294993  443.1455214015781  682.6436366358055

data/test/data/test_collection/SP1_f1.pat

@@ -1,12 +1,12 @@
 > SP1_f1
--0.24435707885585334  -0.6748234046937317  0.8657012535789861  -1.1060188862599292
--1.0631255752097801  -2.1119259694238686  1.0960627561110399  -0.6138563775211981
--0.387227623476054  -2.973985191321805  1.1807800242010371  -4.338927525031567
--4.563896055436894  -2.916163300253228  1.3684371349982631  -5.077972423609655
--2.2369752892820087  -3.719643631330185  1.3510439136452728  -4.8899306705082335
--0.07473964149330914  0.9449196547620103  -2.624685764808605  -0.851098348782244
--1.9643526491643326  -2.9784027708801153  1.3113096718240569  -2.3243342594990253
--4.015548413965584  -3.138426807809667  1.338748858978805  -2.0846739035376483
--0.4450938582835542  -2.2510053061629707  1.126543157436868  -1.7780413702431377
--1.1896356092245055  -1.2251832285630033  1.163676006374752  -1.6080243648157357
--0.5166047365590577  0.7641033353626651  -0.28626775700282125  -0.6825482097865606
+-0.24435707885585292	-0.674823404693731	0.8657012535789866	-1.1060188862599287
+-1.0631255752097797	-2.111925969423868	1.0960627561110403	-0.6138563775211977
+-0.3872276234760535	-2.9739851913218045	1.1807800242010378	-4.338927525031566
+-4.563896055436894	-2.9161633002532277	1.3684371349982638	-5.077972423609655
+-2.2369752892820083	-3.7196436313301846	1.3510439136452734	-4.889930670508233
+-0.07473964149330865	0.944919654762011	-2.6246857648086044	-0.8510983487822436
+-1.9643526491643322	-2.978402770880115	1.3113096718240573	-2.324334259499025
+-4.0155484139655835	-3.1384268078096667	1.3387488589788057	-2.084673903537648
+-0.44509385828355363	-2.2510053061629702	1.1265431574368685	-1.7780413702431372
+-1.1896356092245048	-1.2251832285630027	1.1636760063747527	-1.6080243648157353
+-0.5166047365590571	0.7641033353626657	-0.2862677570028208	-0.68254820978656