mspire-simulator 0.1.2 → 0.2.0

data/lib/ms/sim_peptide.rb

@@ -3,14 +3,17 @@ require 'mspire/isotope/distribution'
 
 module MS
   class Peptide
-    def initialize(sequence, charge)
+    def initialize(sequence, charge, abu = 1.0)
+      @abu = abu
       @p_rt = 0
       @p_int = 0
       @rts = []
       @charge = charge #this is saved in the file name as well
-      
+
       spec = calcSpectrum(sequence, @charge)
-      
+
+      # TODO Ryan: alter this to handle variable and static mass modifications... Add it from the Katamari code
+
       @core_ints = spec.intensities.clone
       @core_mzs = spec.mzs.clone
       @mzs_file = ".m/#{sequence[0]}/#{sequence[0...15]}_#{charge}"
@@ -22,30 +25,30 @@ module MS
       @mass = @mono_mz * @charge
       #U,O,X ???
       amino_acids = ['A','R','N','D','B','C','E','Q','Z','G','H','I',
-		     'L','K','M','F','P','S','T','W','Y','V','J']
+        'L','K','M','F','P','S','T','W','Y','V','J']
       @aa_counts = amino_acids.map do |aa|
-	sequence.count(aa)
+        sequence.count(aa)
       end
       @aa_counts<<0.0
     end
-    
-    attr_reader :mass, :charge, :mono_mz, :core_mzs, :p_rt, :p_int, :core_ints, :hydro, :pi, :aa_counts, :p_rt_i
-    attr_writer :mass, :charge, :mono_mz, :core_mzs, :p_rt, :p_int, :core_ints, :hydro, :pi, :aa_counts, :p_rt_i
-    
+
+    attr_reader :mass, :charge, :mono_mz, :core_mzs, :p_rt, :p_int, :core_ints, :hydro, :pi, :aa_counts, :p_rt_i, :abu, :sx
+    attr_writer :mass, :charge, :mono_mz, :core_mzs, :p_rt, :p_int, :core_ints, :hydro, :pi, :aa_counts, :p_rt_i, :abu, :sx
+
     def to_s
       file = File.open(@mzs_file,"r")
       seq = file.gets.chomp
       file.close
       "Peptide: #{seq}"
     end
-    
+
     def sequence
       file = File.open(@mzs_file,"r")
       seq = file.gets.chomp
       file.close
       seq
     end
-    
+
     #---------------------------------------------------------------------------
     def ints
       file = File.open(@ints_file, "r")
@@ -53,20 +56,20 @@ module MS
       file.close
       ints = []
       line.each do |iso|
-	ints<<iso.chomp.split(/,/).map!{|fl| fl.to_f}
+        ints<<iso.chomp.split(/,/).map!{|fl| fl.to_f}
       end
       return ints
     end
-    
+
     def insert_ints(arr)
       file = File.open(@ints_file, "a")
       arr.each do |val|
-	file.print("#{val},")
+        file.print("#{val},")
       end
       file.print(";")
       file.close
     end
-    
+
     def mzs
       file = File.open(@mzs_file, "r")
       line = file.gets
@@ -74,44 +77,44 @@ module MS
       file.close
       mzs = []
       line.each do |iso|
-	mzs<<iso.chomp.split(/,/).map!{|fl| fl.to_f}
+        mzs<<iso.chomp.split(/,/).map!{|fl| fl.to_f}
       end
       return mzs
     end
-    
+
     def insert_mzs(arr)
       file = File.open(@mzs_file, "a")
       arr.each do |val|
-	file.print("#{val},")
+        file.print("#{val},")
       end
       file.print(";")
       file.close
     end
-    
+
     def rts
       return Sim_Spectra::r_times[@rts[0]..@rts[1]]
     end
-    
+
     def set_rts(a,b)
       @rts = [a,b]
     end
-    
+
     def delete
       if File.exists?(@mzs_file)
-	File.delete(@mzs_file)
+        File.delete(@mzs_file)
       end
       if File.exists?(@ints_file)
-	File.delete(@ints_file)
+        File.delete(@ints_file)
       end
     end
     #---------------------------------------------------------------------------
-    
+
     # Calculates theoretical specturm
     #
     def calcSpectrum(seq, charge)
       #isotope.rb from Dr. Prince
       atoms = countAtoms(seq)
-      
+
       var = ""
       var<<"O"
       var<<atoms[0].to_s
@@ -127,7 +130,7 @@ module MS
       var<<atoms[5].to_s
       var<<"Se"
       var<<atoms[6].to_s
-      
+
       mf = Mspire::MolecularFormula.from_string(var, charge)
       spec = Mspire::Isotope::Distribution.spectrum(mf, :max, 0.001)
 
@@ -135,8 +138,8 @@ module MS
 
       return spec
     end
-    
-      
+
+
     # Counts the number of each atom in the peptide sequence.
     #
     def countAtoms(seq)
@@ -148,33 +151,33 @@ module MS
       p = 0
       se = 0
       seq.each_char do |aa|
-      
-	#poly amino acids
-	#"X" is for any (I exclude uncommon "U" and "O")
-	if aa == "X"
-	  aas = Mspire::Isotope::AA::ATOM_COUNTS.keys[0..19]
-	  aa = aas[rand(20)]
-	#"B" is "N" or "D"
-	elsif aa == "B"
-	  aas = ["N","D"]
-	  aa = aas[rand(2)]
-	#"Z" is "Q" or "E"
-	elsif aa == "Z"
-	  aas = ["Q","E"]
-	  aa = aas[rand(2)]
-	end
-	
-	if aa !~ /A|R|N|D|C|E|Q|G|H|I|L|K|M|F|P|S|T|W|Y|V|U|O/
-	  puts "No amino acid match for #{aa}"
-	else
-	  o = o + Mspire::Isotope::AA::ATOM_COUNTS[aa][:o]
-	  n = n + Mspire::Isotope::AA::ATOM_COUNTS[aa][:n]
-	  c = c + Mspire::Isotope::AA::ATOM_COUNTS[aa][:c]
-	  h = h + Mspire::Isotope::AA::ATOM_COUNTS[aa][:h]
-	  s = s + Mspire::Isotope::AA::ATOM_COUNTS[aa][:s]
-	  p = p + Mspire::Isotope::AA::ATOM_COUNTS[aa][:p]
-	  se = se + Mspire::Isotope::AA::ATOM_COUNTS[aa][:se]
-	end
+
+        #poly amino acids
+        #"X" is for any (I exclude uncommon "U" and "O")
+        if aa == "X"
+          aas = Mspire::Isotope::AA::ATOM_COUNTS.keys[0..19]
+          aa = aas[rand(20)]
+          #"B" is "N" or "D"
+        elsif aa == "B"
+          aas = ["N","D"]
+          aa = aas[rand(2)]
+          #"Z" is "Q" or "E"
+        elsif aa == "Z"
+          aas = ["Q","E"]
+          aa = aas[rand(2)]
+        end
+
+        if aa !~ /A|R|N|D|C|E|Q|G|H|I|L|K|M|F|P|S|T|W|Y|V|U|O/
+          puts "No amino acid match for #{aa}"
+        else
+          o = o + Mspire::Isotope::AA::ATOM_COUNTS[aa][:o]
+          n = n + Mspire::Isotope::AA::ATOM_COUNTS[aa][:n]
+          c = c + Mspire::Isotope::AA::ATOM_COUNTS[aa][:c]
+          h = h + Mspire::Isotope::AA::ATOM_COUNTS[aa][:h]
+          s = s + Mspire::Isotope::AA::ATOM_COUNTS[aa][:s]
+          p = p + Mspire::Isotope::AA::ATOM_COUNTS[aa][:p]
+          se = se + Mspire::Isotope::AA::ATOM_COUNTS[aa][:se]
+        end
       end
       return (o + 1),n,c,(h + 2) ,s,p,se
     end

data/lib/ms/sim_spectra.rb

@@ -7,12 +7,11 @@ require 'ms/sim_feature'
 module MS
   class Sim_Spectra
     def initialize(peptides,opts,one_d = false)
-      @density = opts[:noise_density]
       @data
       @max_mz
-			sampling_rate = opts[:sampling_rate]
-			run_time = opts[:run_time]
-			drop_percentage = opts[:dropout_percentage]
+      sampling_rate = opts[:sampling_rate]
+      run_time = opts[:run_time]
+      drop_percentage = opts[:dropout_percentage]
       #RTS
       var = 0.1/(sampling_rate*2)
       @@r_times = []
@@ -23,43 +22,43 @@ module MS
         spec_time = spec_time + (1/sampling_rate)
       end
       @@r_times = MS::Noise.spec_drops(drop_percentage)
-      
+
       pre_features = MS::Rtgenerator.generateRT(peptides,one_d)
-      
+
       #Features
       features_o = MS::Sim_Feature.new(pre_features,opts,one_d)
       @features = features_o.features
       @data = features_o.data
-      @max_mz = @data.max_by{|key,val| if val != nil;val[0].max;else;0;end}[1][0].max
+      @max_mz = features_o.max_mz
       @spectra = @data.clone
-      
+
       @noise = nil
-      
+
     end
-    
+
     def noiseify
-      @noise = MS::Noise.noiseify(@density,@max_mz)
-      
+      @noise = MS::Noise.noiseify(opts,@max_mz)
+
       @@r_times.each do |k|
-	s_v = @data[k]
-	n_v = @noise[k]
-	if s_v != nil
-	  @spectra[k] = [s_v[0]+n_v[0],s_v[1]+n_v[1]]
-	else
-	  @spectra[k] = [n_v[0],n_v[1]]
-	end
+        s_v = @data[k]
+        n_v = @noise[k]
+        if s_v != nil
+          @spectra[k] = [s_v[0]+n_v[0],s_v[1]+n_v[1]]
+        else
+          @spectra[k] = [n_v[0],n_v[1]]
+        end
       end
-      
+
       return @noise
     end
-    
+
     def self.r_times
       @@r_times
     end
-    
+
     attr_reader :data, :max_mz, :spectra, :noise, :features
     attr_writer :data, :max_mz, :spectra, :noise, :features
-    
+
   end
 end
 

data/lib/ms/sim_trollop.rb

@@ -6,19 +6,19 @@ module MS
       @opts = Trollop::options do
         version "mspire-simulator 0.0.1a (c) 2012 Brigham Young University"
         banner <<-EOS
-        
+
         *********************************************************************
          Description: Simulates ms runs given protein fasta files. Outputs
          a mzML file.
-         
-         
+
+
         Usage:
              mspire-simulator [options] <filenames>+
-             
+
         where [options] are:
         EOS
         opt :digestor, "Digestion Enzyme; one of: \n\t\targ_c,\n \t\tasp_n,
-		asp_n_ambic,
+    asp_n_ambic,
                 chymotrypsin,\n \t\tcnbr,
                 lys_c,\n \t\tlys_c_p,
                 pepsin_a,\n\t\ttryp_cnbr,
@@ -27,42 +27,46 @@ module MS
                 trypsin,\n \t\tv8_e_trypsin,
                 v8_de_trypsin",
                 :default => "trypsin" 
-        opt :sampling_rate, "How many scans per second", :default => 0.5 
-        opt :run_time, "Run time in seconds", :default => 1000.0 
-        opt :noise, "Noise on or off", :default => "true"
-        opt :noise_density, "Determines the density of white noise", :default => 10
-        opt :pH, "The pH that the sample is in - for determining charge", :default => 2.6
-        opt :out_file, "Name of the output file", :default => "test.mzml"
-        opt :contaminants, "Fasta file containing contaminant sequences", :default => "testFiles/contam/hum_keratin.fasta"
-        opt :dropout_percentage, "Defines the percentage of random dropouts in the run. 0.0 <= percentage < 1.0", :default => 0.12
-        opt :shuffle, "Option shuffles the scans to simulate 1d data", :default => "false"
-        opt :one_d, "Turns on one dimension simulation; run_time is automatically set to 300.0", :default => "false"
-        opt :truth, "Determines truth file type; false gives no truth file; one of: xml or csv", :default => "false"
-        opt :front, "Fronting chromatography parameter", :default => 6.65
-        opt :tail, "Tailing chromatography parameter", :default => 0.30
-        opt :mu, "Expected value of the chromatography curve", :default => 25.0
-        opt :wobA, "m/z wobble parameter", :default => 0.001071
-        opt :wobB, "m/z wobble parameter", :default => -0.5430
-        opt :jagA, "intensity variance parameter", :default => 10.34
-        opt :jagC, "intensity variance parameter", :default => 0.00712
-        opt :jagB, "intensity variance parameter", :default => 0.12
-        opt :overlapRange, "range in which to determine overlapping peaks", :default => 1.0724699230489427
-        opt :email, "Email address to send completion messages to", :default => "nil"
-        opt :mzml, "Mzml file to extract simulation parameters from", :default => "nil"
-        opt :generations, "If an mzml file is provided this specifies the number of generations for the curve fitting algorithm", :default => 30000
-        
+                opt :sampling_rate, "How many scans per second", :default => 0.5 
+                opt :run_time, "Run time in seconds", :default => 1000.0 
+                opt :noise, "Noise on or off", :default => "true"
+                opt :noise_density, "Determines the density of white noise", :default => 10
+		opt :noiseMaxInt, "The max noise intensity level", :default => 1000
+		opt :noiseMinInt, "The minimum noise intensity level", :default => 50
+                opt :pH, "The pH that the sample is in - for determining charge", :default => 2.6
+                opt :out_file, "Name of the output file", :default => "test.mzml"
+                opt :contaminants, "Fasta file containing contaminant sequences", :default => "testFiles/contam/hum_keratin.fasta"
+                opt :dropout_percentage, "Defines the percentage of random dropouts in the run. 0.0 <= percentage < 1.0", :default => 0.01
+                opt :shuffle, "Option shuffles the scans to simulate 1d data", :default => "false"
+                opt :one_d, "Turns on one dimension simulation; run_time is automatically set to 300.0", :default => "false"
+                opt :truth, "Determines truth file type; false gives no truth file; one of: xml or csv", :default => "false"
+                opt :front, "Fronting chromatography parameter", :default => 6.65
+                opt :tail, "Tailing chromatography parameter", :default => 0.30
+                opt :mu, "Expected value of the chromatography curve", :default => 25.0
+                opt :wobA, "m/z wobble parameter", :default => 0.001071
+                opt :wobB, "m/z wobble parameter", :default => -0.5430
+                opt :jagA, "intensity variance parameter", :default => 10.34
+                opt :jagC, "intensity variance parameter", :default => 0.00712
+                opt :jagB, "intensity variance parameter", :default => 0.12
+                opt :overlapRange, "range in which to determine overlapping peaks", :default => 1.0724699230489427
+                opt :email, "Email address to send completion messages to", :default => "nil"
+                opt :mzml, "Mzml file to extract simulation parameters from", :default => "nil"
+                opt :generations, "If an mzml file is provided this specifies the number of generations for the curve fitting algorithm", :default => 30000
+                opt :mass_label, "Specify a mass tag pattern", :default => 0
+                opt :modifications, "Use a specific modifications file, or read them from a header of the fasta file, perhaps... TBD..."
+
       end
-    
+
       if @opts[:mzml] != "nil"
         @opts = CurveFit.get_parameters(@opts)
       end
       Trollop::die :sampling_rate, "must be greater than 0" if @opts[:sampling_rate] <= 0
       Trollop::die :run_time, "must be non-negative" if @opts[:run_time] < 0
-      Trollop::die "must supply a .fasta protien sequence file" if ARGV.empty?
+      Trollop::die "must supply a .fasta protein sequence file" if ARGV.empty?
       Trollop::die :dropout_percentage, "must be between greater than or equal to 0.0 or less than 1.0" if @opts[:dropout_percentage] < 0.0 or @opts[:dropout_percentage] >= 1.0
       @opts[:overlapRange] = (@opts[:overlapRange]*10.0**-6)/2.0
     end
-    
+
     def get; @opts; end
   end
 end

data/lib/ms/tr_file_writer.rb

@@ -6,47 +6,51 @@ module MS
   class Txml_file_writer
     def self.write(features,spectra,file_name)
       @spectra = spectra
-      @start = Time.now
       file = File.open("#{file_name}_truth.xml","w")
-      
+
       r_times = spectra.keys.sort
-      
+
       file.puts "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
       file.puts "<simulated_peptides>"
-	total = features.size.to_f
-	features.each_with_index do |fe,k|
-	  sequence = fe.sequence
-	  charge = fe.charge
-	  mzs = fe.mzs
-	  ints = fe.ints
-	  rts = fe.rts
-	  Progress.progress("Writing xml:",(((k/total)*100).to_i))
-	  file.puts "\t<simulated_peptide sequence=\"#{sequence}\" charge=\"#{charge.round}\">"
-	    mzs.each_with_index do |mzs,i|
-	      tags = ""
-	      centroids = ""
-	      tags<<"\t\t<lc_centroids isotopic_index=\"#{i}\">"
-		mzs.each_with_index do |mz,ind|
-		  if ints[i][ind] > 0.9
-		    index = get_ind(mz,rts[ind])
-		    centroids<<"#{r_times.index(rts[ind])},#{index.inspect};"
-		  end
-		end
-	      if centroids != ""
-		tags<<centroids
-		tags<<"</lc_centroids>\n"
-		file<<tags
-	      end
-	    end
-	  file.puts "\t</simulated_peptide>"
-	end
+      total = features.size.to_f
+      prog = Progress.new("Writing xml:")
+      num = 0
+      step = total/100.0
+      features.each_with_index do |fe,k|
+        sequence = fe.sequence
+        charge = fe.charge
+        mzs = fe.mzs
+        ints = fe.ints
+        rts = fe.rts
+        if k > step * (num + 1)
+          num = (((k/total)*100).to_i)
+          prog.update(num)
+        end
+        file.puts "\t<simulated_peptide sequence=\"#{sequence}\" charge=\"#{charge.round}\">"
+        mzs.each_with_index do |mzs,i|
+          tags = ""
+          centroids = ""
+          tags<<"\t\t<lc_centroids isotopic_index=\"#{i}\">"
+          mzs.each_with_index do |mz,ind|
+            if ints[i][ind] > 0.9
+              index = get_ind(mz,rts[ind])
+              centroids<<"#{r_times.index(rts[ind])},#{index.inspect};"
+            end
+          end
+          if centroids != ""
+            tags<<centroids
+            tags<<"</lc_centroids>\n"
+            file<<tags
+          end
+        end
+        file.puts "\t</simulated_peptide>"
+      end
       file.puts "</simulated_peptides>"
       file.close
-      
-      Progress.progress("Writing xml:",100,Time.now-@start)
-      puts ''
+
+      prog.finish!
     end
-    
+
     def self.get_ind(mz,rt)
       index = nil
       if @spectra[rt] != nil
@@ -65,109 +69,118 @@ module MS
       return index
     end
   end
-  
+
   class Tcsv_file_writer
     def self.write(full_spectra,spectra,noise,features,file_name)
-      @start = Time.now
       @spectra = full_spectra
-    
+
       #create indices for real peaks
       ind_hash = create_indicies(features)
-    
+
       #create data structure with indices
       data = data_with_indicies(full_spectra,spectra,noise,ind_hash)
-      
+
       #group by retention time
       data = data.group_by{|d| d[0]}
-      
+
       #write
       file = File.open("#{file_name}_truth.csv","w")
       file.puts "rt,mz,int,index"
       total = data.size.to_f
       count = 0
+      prog = Progress.new("Writing csv(process 2 of 2):")
+      num = 0
+      step = total/100
       data.each_value do |val|
-	Progress.progress("Writing csv(process 2 of 2):",(((count/total)*100).to_i))
-	val.each do |a|
-	  if a[3] >= 1
-	    file.puts "#{a[0]},#{a[1]},#{a[2]},#{a[3]}"
-	  else
-	    file.puts "#{a[0]},#{a[1]},#{a[2]},#{0}"
-	  end
-	end
-	count += 1
+        if count > step * (num + 1)
+          num = (((count/total)*100).to_i)
+          prog.update(num)
+        end
+        val.each do |a|
+          if a[3] >= 1
+            file.puts "#{a[0]},#{a[1]},#{a[2]},#{a[3]}"
+          else
+            file.puts "#{a[0]},#{a[1]},#{a[2]},#{0}"
+          end
+        end
+        count += 1
       end
       file.close
-      
-      Progress.progress("Writing csv:",100,Time.now-@start)
-      puts ''
+      prog.finish!
     end
-    
+
     def self.get_merged_mz(mz,rt)
       m_mz = nil
       int = nil
       mzs = @spectra[rt][0]
       ints = @spectra[rt][1]
       mzs.each_with_index do |m, i|
-	if m == mz
-	  m_mz = mz
-	  int = ints[i]
-	elsif m.class == Hash
-	  if ind = m.values[0].index(mz)
-	    m_mz = [m.keys[0][0],m.keys[0][ind+1]]
-	    int = ints[i].flatten.inject(:+)
-	  end
-	end
+        if m == mz
+          m_mz = mz
+          int = ints[i]
+        elsif m.class == Hash
+          if ind = m.values[0].index(mz)
+            m_mz = [m.keys[0][0],m.keys[0][ind+1]]
+            int = ints[i].flatten.inject(:+)
+          end
+        end
       end
       return m_mz,int
     end
-    
+
     def self.create_indicies(features)
       ind_hash = {}
       features.each_with_index do |pep,i|
-	pep.mzs.each_with_index do |m_ar,j|
-	  m_ar.each do |mz|
-	    ind_hash[mz] = "#{i + 1}.#{j + 1}".to_f
-	  end
-	end
+        pep.mzs.each_with_index do |m_ar,j|
+          m_ar.each do |mz|
+            ind_hash[mz] = "#{i + 1}.#{j + 1}".to_f
+          end
+        end
       end
       return ind_hash
     end
-    
+
     def self.data_with_indicies(full_spectra,spectra,noise,ind_hash)
       count = 1
       time_i = 0.0
       data = []
       total = spectra.length
+      prog = Progress.new("Writing csv(process 1 of 2):")
+      num = 0
+      step = total/100
       spectra.each do |k,v|
-	Progress.progress("Writing csv(process 1 of 2):",(((time_i/total)*100).to_i))
-	
-	merged_d = full_spectra[k]
-	merged_mzs = merged_d[0]
-	merged_ints = merged_d[1]
-	
-	if noise != "false"
-	  n_data = noise[k]
-	end
-	
-	if v != nil
-	  v.each_slice(2) do |m,i|
-	    m.each_with_index do |mz,index|
-	      peak_index = ind_hash[mz]
-	      mz,int = get_merged_mz(mz,k)
-	      data<<[k,mz.inspect,int,peak_index]
-	    end
-	  end
-	end
-	
-	if noise != "false"
-	  n_data.each_slice(2) do |m,i|
-	    m.each_with_index do |mz,index|
-	      mz,int = get_merged_mz(mz,k)
-	      data<<[k,mz.inspect,int,0]
-	    end
-	  end
-	end
-	time_i += 1
+        if time_i > step * (num + 1)
+          num = (((time_i/total)*100).to_i)
+          prog.update(num)
+        end
+
+        merged_d = full_spectra[k]
+        merged_mzs = merged_d[0]
+        merged_ints = merged_d[1]
+
+        if noise != "false"
+          n_data = noise[k]
+        end
+
+        if v != nil
+          v.each_slice(2) do |m,i|
+            m.each_with_index do |mz,index|
+              peak_index = ind_hash[mz]
+              mz,int = get_merged_mz(mz,k)
+              data<<[k,mz.inspect,int,peak_index]
+            end
+          end
+        end
+
+        if noise != "false"
+          n_data.each_slice(2) do |m,i|
+            m.each_with_index do |mz,index|
+              mz,int = get_merged_mz(mz,k)
+              data<<[k,mz.inspect,int,0]
+            end
+          end
+        end
+        time_i += 1
       end
       return data
     end