Module: MS::Weka

Defined in:
lib/ms/rt/weka.rb

Class Method Summary collapse

Class Method Details

.make_int_arff(sourcefile, training) ⇒ Object

James Dalg



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# File 'lib/ms/rt/weka.rb', line 115

def make_int_arff(sourcefile, training)
  sourcefile<<".arff"
  File.open(sourcefile, "wb") do |f| # need to cite f.puts (not %Q)? if so http://www.devdaily.com/blog/post/ruby/how-write-text-to-file-ruby-example
    f.puts %Q{%
%
   @RELATION molecularinfo
   @ATTRIBUTE mz   	NUMERIC
   @ATTRIBUTE charge   NUMERIC
   @ATTRIBUTE mass 	NUMERIC
   @ATTRIBUTE rt   NUMERIC
   @ATTRIBUTE A    NUMERIC
   @ATTRIBUTE R    NUMERIC
   @ATTRIBUTE N    NUMERIC
   @ATTRIBUTE D    NUMERIC
   @ATTRIBUTE B    NUMERIC
   @ATTRIBUTE C    NUMERIC
   @ATTRIBUTE E    NUMERIC
   @ATTRIBUTE Q    NUMERIC
   @ATTRIBUTE Z    NUMERIC
   @ATTRIBUTE G    NUMERIC
   @ATTRIBUTE H    NUMERIC
   @ATTRIBUTE I    NUMERIC
   @ATTRIBUTE L    NUMERIC
   @ATTRIBUTE K    NUMERIC
   @ATTRIBUTE M    NUMERIC
   @ATTRIBUTE F    NUMERIC
   @ATTRIBUTE P    NUMERIC
   @ATTRIBUTE S    NUMERIC
   @ATTRIBUTE T    NUMERIC
   @ATTRIBUTE W    NUMERIC
   @ATTRIBUTE Y    NUMERIC
   @ATTRIBUTE V    NUMERIC
   @ATTRIBUTE intensity  NUMERIC
   @DATA
%
%      }
  end
  training.each do |innerarray|
    CSV.open(sourcefile, "a") do |csv| #derived from sample code http://www.ruby-doc.org/stdlib-1.9.3/libdoc/csv/rdoc/CSV.html
      csv << innerarray #idea may be slightly attributable to http://www.ruby-forum.com/topic/299571
    end
  end
  return sourcefile
end

.make_rt_arff(sourcefile, training) ⇒ Object

James Dalg



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# File 'lib/ms/rt/weka.rb', line 71

def make_rt_arff(sourcefile, training)
  sourcefile<<".arff"
  File.open(sourcefile, "wb") do |f| # need to cite f.puts (not %Q)? if so http://www.devdaily.com/blog/post/ruby/how-write-text-to-file-ruby-example
    f.puts %Q{%
%
   @RELATION molecularinfo
   @ATTRIBUTE A    NUMERIC
   @ATTRIBUTE R    NUMERIC
   @ATTRIBUTE N    NUMERIC
   @ATTRIBUTE D    NUMERIC
   @ATTRIBUTE B    NUMERIC
   @ATTRIBUTE C    NUMERIC
   @ATTRIBUTE E    NUMERIC
   @ATTRIBUTE Q    NUMERIC
   @ATTRIBUTE Z    NUMERIC
   @ATTRIBUTE G    NUMERIC
   @ATTRIBUTE H    NUMERIC
   @ATTRIBUTE I    NUMERIC
   @ATTRIBUTE L    NUMERIC
   @ATTRIBUTE K    NUMERIC
   @ATTRIBUTE M    NUMERIC
   @ATTRIBUTE F    NUMERIC
   @ATTRIBUTE P    NUMERIC
   @ATTRIBUTE S    NUMERIC
   @ATTRIBUTE T    NUMERIC
   @ATTRIBUTE W    NUMERIC
   @ATTRIBUTE Y    NUMERIC
   @ATTRIBUTE V    NUMERIC
   @ATTRIBUTE J    NUMERIC
   @ATTRIBUTE rt    NUMERIC
   @DATA
%
%      }
  end
  training.each do |innerarray|
    CSV.open(sourcefile, "a") do |csv| #derived from sample code http://www.ruby-doc.org/stdlib-1.9.3/libdoc/csv/rdoc/CSV.html
      csv << innerarray #idea may be slightly attributable to http://www.ruby-forum.com/topic/299571
    end
  end
  return sourcefile
end

.predict_ints(db) ⇒ Object 



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# File 'lib/ms/rt/weka.rb', line 40

def predict_ints(db)
  data = []
  aas = "A,R,N,D,B,C,E,Q,Z,G,H,I,L,K,M,F,P,S,T,W,Y,V,J,place_holder"
  rs = db.execute "SELECT mono_mz, charge, mass, p_rt,#{aas} FROM peptides NATURAL JOIN aac" #JOIN aac
  rs.each do |row|
    data<<row
  end

  arff = make_int_arff(Time.now.nsec.to_s,data)

  path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
  dir = path[0..path.size-3].join("/")
  system("java weka.classifiers.trees.M5P -T #{arff} -l #{dir}/lib/weka/M5P.model -p 27 > #{arff}.out")
  system("rm #{arff}")

  #extract what was predicted by weka model
  file = File.open("#{arff}.out","r")
  count = 0
  while line = file.gets
    if line =~ /(\d*\.\d{0,3}){1}/
      p_int = line.match(/(\d*\.\d{0,3}){1}/)[0].to_f
      db.execute "UPDATE peptides SET p_int=#{p_int} WHERE Id='#{count}'"
      count += 1
    end
  end
  system("rm #{arff}.out")
end

.predict_rts(db) ⇒ Object 



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# File 'lib/ms/rt/weka.rb', line 8

def predict_rts(db)
  #mz,charge,intensity,rt,A,R,N,D,B,C,E,Q,Z,G,H,I,L,K,M,F,P,S,T,W,Y,V,J,mass,hydro,pi
  #make arrf file to feed weka model
  data = []
  rs = db.execute "SELECT * FROM aac"
  rs.each do |row|
    row.delete_at(0)
    data<<row
  end

  arff = make_rt_arff(Time.now.nsec.to_s,data)

  path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
  dir = path[0..path.size-3].join("/")
  system("java weka.classifiers.functions.MultilayerPerceptron -T #{arff} -l #{dir}/lib/weka/M5Rules.model -p 24 > #{arff}.out")
  system("rm #{arff}")

  #extract what was predicted by weka model
  file = File.open("#{arff}.out","r")
  count = 0
  while line = file.gets
    if line =~ /(\d*\.\d{0,3}){1}/
      p_rt = line.match(/(\d*\.\d{0,3}){1}/)[0].to_f
      db.execute "UPDATE peptides SET p_rt=#{p_rt} WHERE Id='#{count}'"
      count += 1
    end
  end
  system("rm #{arff}.out")
end