Class: Ms::Xcalibur::Convert::DtaToMgf

Inherits:
Tap::FileTask
  • Object
show all
Includes:
Constants::Libraries
Defined in:
lib/ms/xcalibur/convert/dta_to_mgf.rb

Overview

:startdoc::manifest convert dta files to mgf format Converts a set of .dta files (Sequest format) into an .mgf (Mascot format) file. The conversion is straightforward.

dta format:

[input_file.dta]
353.128 1 
85.354 2.2
87.302 2.8
...

mgf format:

[output_file.mgf]
BEGIN IONS
TITLE=input_file
CHARGE=1
PEPMASS=<calculated>
85.354 2.2
87.302 2.8
...
END IONS

The first line of the dta file specifies the M+H (mh) and charge state (z) of the precursor ion. To convert this to PEPMASS, use (mh + (z-1) * H)/ z) where H is the mass of a proton, ie hydrogen - electron. The mass of a proton is calculated from the constants gem to be ~ 1.007276 Da

Instance Method Summary collapse

Instance Method Details

#process(output_file, *inputs) ⇒ Object 



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# File 'lib/ms/xcalibur/convert/dta_to_mgf.rb', line 41

def process(output_file, *inputs)
  return output_file if inputs.empty?

  dta_files = inputs.collect do |file| 
    if File.directory?(file)
      Dir.glob(File.expand_path(File.join(file, "*.dta")))
    else
      raise "Not a .dta file: #{file}" unless file =~ /\.(dta)$/
      file
    end
  end

  prepare(output_file) 
  File.open(output_file, "wb") do |target|
    h = proton_mass

    dta_files.flatten.each do |file|
      #log_basename(:merging, file)
      lines = File.read(file).split(/\r?\n/)

      # get the mh and z
      mh, z = lines.shift.split(/\s+/)
      mh = mh.to_f
      z = z.to_i

      # add a trailing empty line
      lines << ""

      # make the output
      target << %Q{BEGIN IONS
TITLE=#{File.basename(file)}
CHARGE=#{z}+
PEPMASS=#{(mh + (z-1) * h)/ z}
#{lines.join("\n")}
END IONS

}
    end
  end
  log(:made, output_file)

  output_file
end