Class: Ms::Xcalibur::Convert::RawToDta

Inherits:
Tap::FileTask
  • Object
show all
Defined in:
lib/ms/xcalibur/convert/raw_to_dta.rb

Overview

:startdoc::manifest convert RAW files to dta format Converts a .RAW file to dta files using extract_msn.exe

extract_msn.exe is an Xcalibur/BioWorks tool that extracts spectra from .RAW files into .dta (Sequest) format and must be installed for RawToDta to work. RawToDta was developed against extract_msn version 4.0. You can check if extract_msn is installed at the default location, as well as determine the

version of your executable using:

% tap run -- xcalibur/convert/raw_to_dta  --extract_msn_help

Constant Summary collapse

CONFIG_MAP = 
[
  [:first_scan, 'F'],
  [:last_scan, 'L'],
  [:lower_MW, 'B'],
  [:upper_MW, 'T'],
  [:precursor_mass_tol, 'M'],
  [:num_allowed_intermediate_scans_for_grouping, 'S'],
  [:charge_state, 'C'],
  [:num_required_group_scans, 'G'],
  [:num_ions_required, 'I'],
  [:output_path, 'D'],
  [:intensity_threshold, 'E'],
  [:use_unified_search_file, 'U'],
  [:subsequence, 'Y'],
  [:write_zta_files, 'Z'],
  [:perform_charge_calculations, 'K'],
  [:template_file, 'O'],
  [:options_string, 'A'],
  [:minimum_signal_to_noise, 'R'],
  [:minimum_number_of_peaks, 'r']
]

Instance Method Summary collapse

Instance Method Details

#cmd(input_file, output_dir = nil) ⇒ Object

Formats the extract_msn.exe command using the specified input_file, and the current configuration. A default output directory can be specified using output_dir; it will not override a configured output directory.

Note that output_dir should be an EXISTING filepath or relative filepath. execute_msn.exe will not generate .dta files if the

output_dir doesn’t exist.



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# File 'lib/ms/xcalibur/convert/raw_to_dta.rb', line 108

def cmd(input_file, output_dir=nil)
  args = []
  args << "\"#{normalize extract_msn}\""
  args << cmd_options(output_dir)
  args << "\"#{normalize input_file}\""

  args.join(' ')
end

#cmd_options(output_dir = nil) ⇒ Object

Formats command options for extract_msn.exe using the current configuration. Configurations are mapped to their single-letter keys using CONFIG_MAP.

A default output_dir can be specified for when config is not specified.



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# File 'lib/ms/xcalibur/convert/raw_to_dta.rb', line 76

def cmd_options(output_dir=nil)
  options = CONFIG_MAP.collect do |key, flag|
    value = (flag == "D" ? output_dir : config[key])
    next unless value

    # formatting consists of stringifying the value argument, or
    # in escaping the value if the arguement is a path
    formatted_value = case key
    when :use_unified_search_file, :perform_charge_calculations, :write_zta_files
      "" # no argument
    when :output_path, :template_file 
      # path argument, escape
      "\"#{normalize value}\""  
    else 
      # number or string, simply stringify
      value.to_s
    end

    "-#{flag}#{formatted_value}"
  end

  options.compact.join(" ")
end

#normalize(path) ⇒ Object

Expands the input path and converts all forward slashes (/) to backslashes () to make it into a Windows-style path.



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# File 'lib/ms/xcalibur/convert/raw_to_dta.rb', line 67

def normalize(path)
  File.expand_path(path).gsub(/\//, "\\")
end

#process(input_file, output_dir = nil) ⇒ Object 



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# File 'lib/ms/xcalibur/convert/raw_to_dta.rb', line 117

def process(input_file, output_dir=nil)
  extname = File.extname(input_file)
  raise "Expected .RAW file: #{input_file}" unless  extname =~ /\.RAW$/i

  # Target the output to a directory with the same basename 
  # as the raw file, unless otherwise specified.
  output_dir = input_file.chomp(File.extname(input_file)) if output_dir == nil

  mkdir(output_dir)
  command = cmd(input_file, output_dir)

  log :sh, command
  if app.quiet
    capture_sh(command, true)
  else
    sh(command)
    puts ""  # add extra line to make logging nice
  end

  # This may select additional .dta files that existed before raw_to_dta
  # TODO - maybe read lcq_dta for files? 
  Dir.glob( File.expand_path(File.join(output_dir, "*.dta")) ) 
end