ms-spectral_summing 0.0.1 → 0.0.2

data/bin/spectral_summing.rb

@@ -0,0 +1,158 @@
+#!/usr/bin/env ruby
+Spectrum = Struct.new(:spectrum, :scan_num, :scan_time, :scan_range, :precursor_mass, :charge_states, :intensities, :mz_values)
+
+class Parser
+	attr_accessor :spectra
+	def initialize(file)
+		@file = file
+	end
+	def parse(file = nil)
+		file ||= @file
+		require 'ms/msrun'
+		@spectra = []
+		Ms::Msrun.open(file) do |ms|
+			ms.each(:ms_level => 2) do |scan|
+				@spectra << Spectrum.new(scan, scan.num, scan.time, (scan.start_mz..scan.end_mz), scan.precursor.mz, scan.precursor.charge_states, scan.spectrum.intensities, scan.spectrum.mzs)
+			end
+		end
+	end
+	def parse_by_scan_num(scan_nums, file = nil)
+		file ||= @file
+		require 'ms/msrun'
+		@spectra = []
+		Ms::Msrun.open(file) do |ms|
+			ms.each(:ms_level => 2) do |scan|
+				if scan_nums.include?(scan.num)
+					@spectra << Spectrum.new(scan, scan.num, scan.time, (scan.start_mz..scan.end_mz), scan.precursor.mz, scan.precursor.charge_states, scan.spectrum.intensities, scan.spectrum.mzs)
+				end
+			end
+		end
+	end
+end
+
+class Combiner 
+	Defaults = {:bin_window => 0.1, :window_size => 4, :precursor_mass_tolerance_in_ppm =>	10, :tolerant => false}
+	attr_accessor :output_spectra
+	def initialize(spectra = nil, opts = {})
+		@spectra = spectra
+		@opts = Defaults.merge(opts)
+	end
+	def combine(spectrum1, spectrum2)
+		tolerance = calculate_daltons_from_ppm(spectrum1.precursor_mass, @opts[:precursor_mass_tolerance_in_ppm] )
+		if tolerance.include?(spectrum2.precursor_mass) or @opts[:tolerant]
+			data_arr = summer(spectrum1.mz_values, spectrum1.intensities, spectrum2.mz_values, spectrum2.intensities)
+		end
+		data_arr
+	end
+	def summer(x1,y1,x2,y2) # What should this return?
+		endpoints = (x1+x2).each.minmax
+		bin_width = @opts[:bin_window]
+		num_bins = ((endpoints.last - endpoints.first)/bin_width).ceil
+		data_x = [endpoints.first+bin_width/2.0]
+		data_y = Array.new(num_bins, 0)
+		j, k = 0,0
+		one = [x1,y1]; two = [x2,y2]
+		if x1.first == endpoints.first
+			data_x[0] = x1.first
+			data_y[0] += y1.first
+			y1[0] = 0
+		elsif x2.first == endpoints.first
+			data_x[0] = x2.first
+			data_y[0] += y2.first
+			y2[0] = 0
+		end
+		(1..num_bins-1).each do |i|
+			data_x[i] = data_x[i-1] + bin_width 
+			check = data_x[i] + bin_width/2.0
+			#puts "check= #{check}"
+			if one.first[j]
+				while one.first[j] < check 
+					data_y[i] += one.last[j]
+					j += 1
+					break if one.first[j].nil?
+				end
+			end
+			if two.first[k]
+				while two.first[k] < check
+					data_y[i] += two.last[k]
+					k += 1
+					break if two.first[k].nil?
+				end
+			end
+		end
+		[data_x, data_y]
+	end
+	def combine_for_more_combining(spectrum1, spectrum2)
+		arr = combine(spectrum1, spectrum2)
+		joined_spectrum = Spectrum.new()
+		joined_spectrum.precursor_mass = (spectrum1.precursor_mass + spectrum2.precursor_mass)/2.0
+		joined_spectrum.mz_values = arr.first
+		joined_spectrum.intensities = arr.last
+# Spectrum = Struct.new(:spectrum, :scan_num, :scan_time, :scan_range, :precursor_mass, :charge_states, :intensities, :mz_values)
+		joined_spectrum
+	end
+	def calculate_daltons_from_ppm(mass, ppm)
+		diff = ppm*mass/1e6
+		(mass-diff)..(mass+diff)
+	end
+	def to_mgf(spectrum, filename)
+		File.open(filename,'w') do |out|
+			out.puts "BEGIN IONS"
+			out.puts "TITLE=Spec1:#{spectrum.precursor_mass}_#{spectrum.charge_states.first}"
+			out.puts "CHARGE=#{spectrum.charge_states.to_s}+"
+			# our current mzML parser doesn't have scan.time implemented...
+			spectrum.mz_values.each_with_index do |mz, i|
+				intensity = spectrum.intensities[i]
+				out.puts "#{"%.5f" % mz}/t#{"%.5f" % intensity}" unless intensity == 0
+			end
+			out.puts "END IONS"
+		end
+	end
+	def combine_to_mgf(spectrum1, spectrum2, filename)   # Thanks JOHN!!! Ms-Msrun 0.3.6
+		results = combine(spectrum1, spectrum2)
+		File.open(filename, 'w') do |out|
+			out.puts "BEGIN IONS"
+			out.puts "TITLE=Spec1:#{spectrum1.precursor_mass}_Spec2:#{spectrum2.precursor_mass}.#{spectrum1.scan_num}_#{spectrum2.scan_num}_#{spectrum1.charge_states.first}"
+			out.puts "CHARGE=#{spectrum1.charge_states.to_s}+"
+			# our current mzML parser doesn't have scan.time implemented...
+			results.first.each_with_index do |mz, i|
+				intensity = results.last[i]
+				out.puts "#{"%.5f" % mz}/t#{"%.5f" % intensity}" unless intensity == 0
+			end
+			out.puts "END IONS"
+		end
+	end
+end
+
+if ARGV.size == 0 or ARGV.size % 2 != 0
+	puts "Usage: #{__FILE__} input_file.mzXML scan_nums.txt input_file2.mzXML scan_nums2.txt ... "
+	puts "NOTE: scan_nums.txt files must have a new line break between each integer value."
+	puts 'Returns input_file_input_file2_..._input_file(n).mgf'
+	exit
+else
+	mzXMLs = []
+	scan_nums = []
+	while ARGV.size > 0
+		mzXMLs << ARGV.shift
+		scan_nums << ARGV.shift
+	end
+	scan_nums.map {|file|	IO.readlines(file) }
+# Parse the files and put the data into spectra objects, held within the list of all spectra to combine.
+	spectras = []
+	mzXML.each_with_index do |file, i|
+		@parse_object = Parser.new(file)
+		@parse_object.parse_by_scan_num(scan_nums[i])
+		spectras << @parse_object.spectra
+	end
+	combined_spectrum = spectras.shift
+	combiner = Combiner.new(combined_spectrum)
+	spectras.each do |spectrum|
+		combined_spectrum = combiner.combine_for_more_combining(combined_spectrum, spectrum)
+	end
+	combiner.to_mgf(combined_spectrum, 'combined_multiple_files.mgf')
+end
+
+		
+
+
+	

metadata

@@ -2,7 +2,7 @@
 name: ms-spectral_summing
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors: 
 - Ryan M Taylor
@@ -25,6 +25,7 @@ files:
 - README.rdoc
 - LICENSE.txt
 - lib/spectral_summing.rb
+- bin/spectral_summing.rb
 homepage: https://github.com/princelab/spectral_summing
 licenses: []