Module: Ms::Sequest::Srf::Search

Included in:
Ms::Sequest::Srf
Defined in:
lib/ms/sequest/srf/search.rb,
lib/ms/sequest/srf/search.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/search.rb', line 112

def self.commandline(argv, progname=$0)
  opt = {
    :format => 'mgf'
  }
  opts = OptionParser.new do |op|
    op.banner = "usage: #{File.basename(__FILE__)} <file>.srf ..."
    op.separator "outputs: <file>.mgf ..."
    op.on("-f", "--format <mgf|dta>", "the output format (default: #{opt[:format]})") {|v| opt[:format] = v }
    op.on("-o", "--outfiles <String,...>", Array, "comma list of output files or directories") {|v| opt[:outfiles] = v }
  end

  opts.parse!(argv)

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

  format = opt[:format]

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

  argv.each_with_index do |srf_file,i|
    base = srf_file.chomp(File.extname(srf_file))
    newfile = 
      if opt[:outfiles]
        opt[:outfiles][i]
      else
        case format
        when 'dta'
          base
        when 'mgf'
          base << '.' << format
        end
      end
    srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )    # options just speed up reading since we don't need .out info anyway

    case format
    when 'mgf'
      srf.to_mgf(newfile)
    when 'dta'
      srf.to_dta(newfile)
    end
  end
end

Instance Method Details

#to_dta(out_folder = nil, compress = nil) ⇒ Object

not given an out_folder, will make one with the basename compress may be: :zip, :tgz, or nil (no compression) :zip requires gem rubyzip to be installed and is very bloated as it writes out all the files first! :tgz requires gem archive-tar-minitar to be installed


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# File 'lib/ms/sequest/srf/search.rb', line 47

def to_dta(out_folder=nil, compress=nil)
  outdir = 
    if out_folder ; out_folder
    else base_name
    end

  case compress
  when :tgz
    begin
      require 'archive/tar/minitar'
    rescue LoadError
      abort "need gem 'archive-tar-minitar' installed' for tgz compression!\n#{$!}"
    end
    require 'archive/targz'  # my own simplified interface!
    require 'zlib'
    names = index.map do |i_ar|
      [outdir, '/', [base_name, *i_ar].join('.'), '.dta'].join('')
    end    #Archive::Targz.archive_as_files(outdir + '.tgz', names, dta_file_data)


    tgz = Zlib::GzipWriter.new(File.open(outdir + '.tgz', 'wb'))

    Archive::Tar::Minitar::Output.open(tgz) do |outp|
      dta_files.each_with_index do |dta_file, i|
        Archive::Tar::Minitar.pack_as_file(names[i], dta_file.to_dta_file_data, outp)
      end
    end
  when :zip
    begin
      require 'zip/zipfilesystem'
    rescue LoadError
      abort "need gem 'rubyzip' installed' for zip compression!\n#{$!}"
    end    #begin ; require 'zip/zipfilesystem' ; rescue LoadError, "need gem 'rubyzip' installed' for zip compression!\n#{$!}" ; end

    Zip::ZipFile.open(outdir + ".zip", Zip::ZipFile::CREATE) do |zfs|
      dta_files.zip(index) do |dta,i_ar|
        #zfs.mkdir(outdir)
        zfs.get_output_stream(outdir + '/' + [base_name, *i_ar].join('.') + '.dta') do |out|
          dta.write_dta_file(out)          #zfs.commit

        end
      end
    end
  else  # no compression
    FileUtils.mkpath(outdir)
    Dir.chdir(outdir) do
      dta_files.zip(index) do |dta,i_ar|
        File.open([base_name, *i_ar].join('.') << '.dta', 'wb') do |out|
          dta.write_dta_file(out)
        end
      end
    end
  end
end

#to_mgf(filename = nil) ⇒ Object

Writes an MGF file to given filename or base_name + '.mgf' if no filename given.

This mimicks the output of merge.pl from mascot The only difference is that this does not include the “rn” that is found after the peak lists, instead, it uses “n” throughout the file (thinking that this is preferable to mixing newline styles!)


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# File 'lib/ms/sequest/srf/search.rb', line 18

def to_mgf(filename=nil)
  filename =
    if filename ; filename
    else
      base_name + '.mgf'
    end
  h_plus = Ms::Mass::MASCOT_H_PLUS
  File.open(filename, 'wb') do |out|
    dta_files.zip(index) do |dta, i_ar|
      chrg = dta.charge
      out.print "BEGIN IONS\n"
      out.print "TITLE=#{[base_name, *i_ar].push('dta').join('.')}\n"
      out.print "CHARGE=#{chrg}+\n"
      out.print "PEPMASS=#{(dta.mh+((chrg-1)*h_plus))/chrg}\n"
      peak_ar = dta.peaks.unpack('e*')
      (0...(peak_ar.size)).step(2) do |i|
        out.print( peak_ar[i,2].join(' '), "\n")
      end
      out.print "END IONS\n"
      out.print "\n"
    end
  end
end