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

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

Overview

:startdoc::task convert dta files to mgf format

Converts a set of dta files (Sequest format) into an mgf (Mascot format) file. By default the mgf file is printed to $stdout, so redirection is a good way to save the results.

% tap run -- dta_to_mgf ... > results.mgf

Alternatively, specify the output file using the output configuration.

Conversion

The dta -> mgf 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(*dta_files) ⇒ Object 



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# File 'lib/ms/xcalibur/convert/dta_to_mgf.rb', line 54

def process(*dta_files)
  prepare(output) if output.kind_of?(String)
  open_io(output, 'w') do |target|
    target.binmode
    
    log :convert, "#{dta_files.length} dta files"
    dta_files.each do |file|
      app.check_terminate
      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) * proton_mass)/ z}
#{lines.join("\n")}
END IONS

}
    end
  end
  output
end