Module: MS::Sequest::Srf::Sqt

Included in:
MS::Sequest::Srf
Defined in:
lib/ms/sequest/srf/sqt.rb,
lib/ms/sequest/srf/sqt.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.commandline(argv, progname = $0) ⇒ Object 



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# File 'lib/ms/sequest/srf/sqt.rb', line 177

def self.commandline(argv, progname=$0)
  opt = {
    :filter => true
  }
  opts = OptionParser.new do |op|
    op.banner = "usage: #{progname} [OPTIONS] <file>.srf ..."
    op.separator "output: <file>.sqt ..."
    op.separator ""
    op.separator "options:"
    op.on("-d", "--db-info", "calculates num aa's and md5sum on db") {|v| opt[:db_info] = v }
    op.on("-p", "--db-path <String>", "If you need to specify the database path") {|v| opt[:new_db_path] = v }
    op.on("-u", "--db-update", "update the sqt file to reflect --db_path") {|v| opt[:db_update] = v }
    op.on("-n", "--no-filter", "by default, pephit must be within peptide_mass_tolerance",  "(defined in sequest.params) to be included.  Turns this off.") { opt[:filter] = false }
    op.on("-o", "--outfiles <first,...>", Array, "Comma list of output filenames") {|v| opt[:outfiles] = v }
    op.on("-r", "--round", "round floating point values reasonably") {|v| opt[:round] = v }
  end
  opts.parse!(argv)

  if argv.size == 0
    puts(opts) || exit
  end

  if opt[:outfiles] && (opt[:outfiles].size != argv.size)
    raise "if outfiles specified, outfiles must be same size as number of input files"
  end

  argv.each_with_index do |srf_file,i|
    outfile = 
      if opt[:outfiles]
        opt[:outfiles][i]
      else
        base = srf_file.chomp(File.extname(srf_file))
        base + '.sqt'
      end

    srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
    srf.to_sqt(outfile, :db_info => opt[:db_info], :new_db_path => opt[:new_db_path], :update_db_path => opt[:db_update], :round => opt[:round])
  end
end

Instance Method Details

#to_sqt(out_filename = nil, opts = {}) ⇒ Object

the out_filename will be the base_name + .sqt unless ‘out_filename’ is defined :round => round floating point numbers etc…



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# File 'lib/ms/sequest/srf/sqt.rb', line 16

def to_sqt(out_filename=nil, opts={})
  # default rounding precision (Decimal Places)
  tic_dp = 2
  mh_dp = 7
  xcorr_dp = 5
  sp_dp = 2
  dcn_dp = 5

  defaults = {:db_info=>false, :new_db_path=>nil, :update_db_path=>false, :round=>false}
  opt = defaults.merge(opts)

  outfile =
    if out_filename
      out_filename
    else
      base_name + '.sqt'
    end
  invariant_ordering = %w(SQTGenerator SQTGeneratorVersion Database FragmentMasses PrecursorMasses StartTime) # just for readability and consistency
  fmt = 
    if params.fragment_mass_type == 'average' ; 'AVG'
    else ; 'MONO'
    end
  pmt =
    if params.precursor_mass_type == 'average' ; 'AVG'
    else ; 'MONO'
    end

  mass_index = params.mass_index
  static_mods = params.static_mods.map do |k,v|
    key =  k.split(/_/)[1]
    if key.size == 1
      key + '=' + (mass_index[key] + v.to_f).to_s
    else
      key + '=' + v
    end
  end

  dynamic_mods = []
  header.modifications.scan(/\((.*?)\)/) do |match|
    dynamic_mods << match.first.sub(/ /,'=')
  end
  plural = {
    'StaticMod' => static_mods,
    'DynamicMod' => dynamic_mods,  # example as diff mod
    'Comment' => ['Created from Bioworks .srf file']
  }

  db_filename = header.db_filename.sub(/\.hdr$/, '') # remove the .hdr postfix
  db_filename_in_sqt = db_filename
  if opt[:new_db_path]
    db_filename = File.join(opt[:new_db_path], File.basename(db_filename.gsub('\\', '/')))
    if opt[:update_db_path]
      db_filename_in_sqt = File.expand_path(db_filename)
      warn "writing Database #{db_filename} to sqt, but it does not exist on this file system" unless File.exist?(db_filename) 
    end
  end

  apmu = 
    case params.peptide_mass_units 
    when '0' ; 'amu' 
    when '1' ; 'mmu'
    when '2' ; 'ppm'
    end

  hh =  {
    'SQTGenerator' => "mspire: ms-sequest",
    'SQTGeneratorVersion' => MS::Sequest::VERSION,
    'Database' => db_filename_in_sqt,
    'FragmentMasses' => fmt,
    'PrecursorMasses' => pmt,
    'StartTime' => '',  # Bioworks 3.2 also leaves this blank...
    'Alg-PreMassTol' => params.peptide_mass_tolerance,
    'Alg-FragMassTol' => params.fragment_ion_tolerance,
    'Alg-PreMassUnits' => apmu, ## mine
    'Alg-IonSeries' => header.ion_series.split(':').last.lstrip,
    'Alg-Enzyme' => header.enzyme.split(':').last,
    'Alg-MSModel' => header.model,
  }

  if opt[:db_info]
    if File.exist?(db_filename)
      reply = MS::Sequest::Sqt.db_info(db_filename)
      %w(DBSeqLength DBLocusCount DBMD5Sum).zip(reply) do |label,val|
        hh[label] = val
      end
    else
      warn "file #{db_filename} does not exist, no extra db info in header!"
    end
  end

  has_hits = (self.out_files.size > 0)
  if has_hits
    # somewhat redundant with above, but we can get this without a db present!
    hh['DBLocusCount'] = self.out_files.first.db_locus_count
  end

  File.open(outfile, 'w') do |out|
    # print the header:
    invariant_ordering.each do |iv|
      out.puts ['H', iv, hh.delete(iv)].join("\t")
    end
    hh.each do |k,v|
      out.puts ['H', k, v].join("\t")
    end
    plural.each do |k,vals|
      vals.each do |val|
        out.puts ['H', k, val].join("\t")
      end
    end

    ##### SPECTRA
    time_to_process = '0.0'
    #########################################
    # NEED TO FIGURE OUT: (in spectra guy)
    #    * Lowest Sp value for top 500 spectra
    #    * Number of sequences matching this precursor ion 
    #########################################

    manual_validation_status = 'U'
    self.out_files.zip(dta_files) do |out_file, dta_file|
      # don't have the time to process (using 0.0 like bioworks 3.2)
      dta_file_mh = dta_file.mh
      out_file_total_inten = out_file.total_inten
      out_file_lowest_sp = out_file.lowest_sp
      if opt[:round]
        dta_file_mh = dta_file_mh.round(mh_dp)
        out_file_total_inten = out_file_total_inten.round(tic_dp)
        out_file_lowest_sp = out_file_lowest_sp.round(sp_dp)
      end

      out.puts ['S', out_file.first_scan, out_file.last_scan, out_file.charge, time_to_process, out_file.computer, dta_file_mh, out_file_total_inten, out_file_lowest_sp, out_file.num_matched_peptides].join("\t")
      out_file.hits.each_with_index do |hit,index|
        hit_mh = hit.mh
        hit_deltacn_orig_updated = hit.deltacn_orig_updated
        hit_xcorr = hit.xcorr
        hit_sp = hit.sp
        if opt[:round]
          hit_mh = hit_mh.round(mh_dp)
          hit_deltacn_orig_updated = hit_deltacn_orig_updated.round(dcn_dp)
          hit_xcorr = hit_xcorr.round(xcorr_dp)
          hit_sp = hit_sp.round(sp_dp)
        end
        # note that the rank is determined by the order..
        out.puts ['M', index+1, hit.rsp, hit_mh, hit_deltacn_orig_updated, hit_xcorr, hit_sp, hit.ions_matched, hit.ions_total, hit.sequence, manual_validation_status].join("\t")
        hit.proteins.each do |prot|
          out.puts ['L', prot.first_entry].join("\t")
        end
      end
    end
  end # close the filehandle
end