Class: MS::Sim_Digester

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sim_digester.rb

Instance Method Summary collapse

Constructor Details

#initialize(opts, db) ⇒ Sim_Digester

Returns a new instance of Sim_Digester.



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# File 'lib/ms/sim_digester.rb', line 12

def initialize(opts,db)
  @db = db
  @db.execute "CREATE TABLE IF NOT EXISTS digested(prot_id INTEGER PRIMARY KEY,header TEXT, abu REAL, sequence TEXT, peptides TEXT)"
  @digestor = opts[:digestor]
  @pH = opts[:pH]
  @missed_cleavages = opts[:missed_cleavages]
  @modifications = Modifications.new(opts[:modifications]).modifications
  @digested = nil
end

Instance Method Details

#create_digested(file) ⇒ Object 



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# File 'lib/ms/sim_digester.rb', line 22

def create_digested(file)
  abundances = []
  headers = []
  inFile = File.open(file,"r")
  seq = ""
  inFile.each_line do |sequence| 
    if sequence =~ />/
      headers<<sequence
      num = sequence.match(/\#.+/).to_s.chomp.gsub('#','')
      if num != ""
        abundances<<(num.to_f)*10.0**-2
      else
        abundances<<1.0
      end
    sequence
    seq = seq<<";"
    elsif sequence == "/n"; else
      seq = seq<<sequence.chomp.upcase
    end
  end
  inFile.close

  proteins = seq.split(/;/).delete_if{|str| str == ""}

  trypsin = Mspire::Digester[@digestor]

  @digested = []
  proteins.each_with_index do |prot,index|
    dig = trypsin.digest(prot,@missed_cleavages) # two missed cleavages for fig 6
    @db.execute "INSERT INTO digested(header,abu,sequence,peptides) VALUES(\"#{headers[index]}\",#{abundances[index]},\"#{prot}\",'#{dig}')"
    dig.each do |d|
      d.abu = abundances[index]
      d.prot_id = index
      @digested<<d
    end
  end
  proteins.clear
  dige = @digested.uniq!
  
  num_digested = @digested.size
  puts "Number of peptides: #{num_digested}"
end

#digest(file) ⇒ Object 



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# File 'lib/ms/sim_digester.rb', line 65

def digest(file)
  prog = Progress.new("Creating peptides '#{file}':")
  create_digested(file)

  i = 0
  count = 0
  num = 0
  total = @digested.size
  step = total/100.0
  @digested.each do |peptide_seq|
      if count > step * (num + 1)
        num = ((count/total.to_f)*100.0).to_i
        prog.update(num)
      end

    charge_ratio = charge_at_pH(identify_potential_charges(peptide_seq), @pH)
    charge_f = charge_ratio.floor
    charge_c = charge_ratio.ceil
    peptide_f = MS::Peptide.new(peptide_seq, charge_f, peptide_seq.abu,@db,i,peptide_seq.prot_id,@modifications) if charge_f != 0
    i += 1 if charge_f != 0
    peptide_c = MS::Peptide.new(peptide_seq, charge_c, peptide_seq.abu,@db,i,peptide_seq.prot_id,@modifications) if charge_c != 0
    i += 1 if charge_c != 0

    count += 1
  end
  prog.finish!
end