Module: Ms::Msrun::Search

Included in:
Ms::Msrun
Defined in:
lib/ms/msrun/search.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.convert(format, file, opts = {}) ⇒ Object

convenience method to convert a file to a search format

Examples:

Ms::Msrun::Search.convert(:mgf, "myfilename.mzXML", :run_id => 25, :run_id_cat => '__')
# writes to the file: "myfilename__25.mgf"

Parameters:

  • format (Symbol) —

    valid format symbol

  • file (String) —

    the filename (relative or absolute)

  • opts (Hash) (defaults to: {}) —

    other options taken by Search:to_search

Options Hash (opts):

  • :run_id (Object) —

    concatenated to output filename with :run_id_cat

  • :run_id_cat (String) — default: '.' —

    concatenate run_id



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

def self.convert(format, file, opts={})
  opts[:run_id_cat] ||= '.'
  new_filename = file.chomp(File.extname(file))
  if opts[:run_id]
    new_filename << opts[:run_id_cat].to_s << opts[:run_id].to_s
  end
  new_filename << '.' << format.to_s

  search_opts = {:output => new_filename}.merge(opts)
  [:run_id, :run_id_cat].each {|s| search_opts.delete(s) }

  Ms::Msrun.open(file) do |ms|
    ms.to_search(format, search_opts)
  end
end

Instance Method Details

#get_vals(opts, scan) ⇒ Object

Factored out method. Simply serves to reduce the size of to_search



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# File 'lib/ms/msrun/search.rb', line 159

def get_vals(opts, scan)
  if opts[:determine_plus_ones]
    # tic under precursor > 95% and true = save the spectrum info
    if scan.plus1?(0.95)
      opts[:charge_states] = [1]
    end
  end
  
  chrg_sts = scan.precursor.charge_states
  if chrg_sts.nil? || !chrg_sts.first.is_a?(Integer)
    chrg_sts = opts[:charge_states_for_unknowns]
  end
  
  pmz = scan.precursor && scan.precursor.mz
  
  [opts, chrg_sts, pmz]
end

#mgf_header(out, scan, sn, z, prec_string, pmz, rtinseconds = nil) ⇒ Object

Creates the mgf-type spectrum header



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# File 'lib/ms/msrun/search.rb', line 107

def mgf_header(out, scan, sn, z, prec_string, pmz, rtinseconds=nil)
  out.puts "BEGIN IONS"
  out.puts "TITLE=#{self.parent_basename_noext}.#{sn}.#{sn}.#{z}"
  out.puts "CHARGE=#{z}+"
  # our current mzML parser doesn't have scan.time implemented...
  out.puts "RTINSECONDS=#{rtinseconds}" if rtinseconds
  out.printf(prec_string, pmz, scan.precursor.intensity)
end

#ms2_header(out, scan, sn, z, mh, pmz) ⇒ Object

Creates the ms2-type spectrum header



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# File 'lib/ms/msrun/search.rb', line 117

def ms2_header(out, scan, sn, z, mh, pmz)
  [['S', sn, sn, pmz], ['I', 'RTime', scan.time], ['Z', z, mh]].each do |ar|
    out.puts ar.join("\t")
  end
end

#set_opts(opts) ⇒ Object

Sets options and other variables to be used by the to_* methods.

Parameters:

  • opts (Hash) —

    a customizable set of options

Options Hash (opts):

  • :included_scans (Array) —

    only include a subset of scans in the output (:ms_levels precedes :included_scans)



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# File 'lib/ms/msrun/search.rb', line 125

def set_opts(opts)
  opts = {
    :retention_times => true,  # includes retention time if applicable
    :filter_zero_intensity => true,
    :output => nil,  # an output file or io object
    :bottom_mh => 0.0,
    :top_mh => nil,
    :ms_levels => (2..-1),  # range or intger, -1 at end will be substituted for last level
    :min_peaks => 0,
    :prec_mz_precision => 6,
    :prec_int_precision => 6,
    :frag_mz_precision => 5,
    :frag_int_precision => 1,
    :charge_states_for_unknowns => [2,3],
    :determine_plus_ones => false,
    :included_scans => nil 
  }.merge(opts)
  
  if opts[:top_mh].nil? || opts[:top_mh] == -1
    opts[:top_mh] = nil
  end
  
  if opts[:last_scan].nil? or opts[:last_scan] == -1
    opts[:last_scan] = self.scan_nums.last
  end
  
  if !opts[:ms_levels].is_a?(Integer) && opts[:ms_levels].last == -1
    opts[:ms_levels] = ((opts[:ms_levels].first)..(scan_counts.size-1))
  end
  
  opts
end

#to_mgf(opts = {}) ⇒ Object

Returns a string unless :output given (may be a String (filename) or a writeable IO object in which case the data is written to file or io and the number of spectra written is returned



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# File 'lib/ms/msrun/search.rb', line 37

def to_mgf(opts={})
  to_search(:mgf, opts)
end

#to_ms2(opts = {}) ⇒ Object

same as to_mgf, but for the ms2 format



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# File 'lib/ms/msrun/search.rb', line 42

def to_ms2(opts={})
  to_search(:ms2, opts)
end

#to_search(format, opts) ⇒ Object

performs the common actions for the different formats (currently :mgf and :ms2), and calls the command for the given format recognizes: 

:output => file to write to
:included_scans => Array of scan numbers
:filter_zero_intensity => remove peaks whose intensity is zero
:bottom_mh => lowest mh value to consider
:top_mh => highest mh value to consider



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# File 'lib/ms/msrun/search.rb', line 54

def to_search(format, opts)

  # set up included_scans for fast access
  if opts[:included_scans]
    included_scans = []
    opts[:included_scans].each {|num| included_scans[num] = true }
  end

  opts = set_opts(opts)
  
  sep = ' '
  frag_string = "%0.#{opts[:frag_mz_precision]}f%s%0.#{opts[:frag_int_precision]}f\n"
  mgf_prec_string = "PEPMASS=%0.#{opts[:prec_mz_precision]}f %0.#{opts[:prec_int_precision]}f\n"
  retention_times = opts[:retention_times]
  
  any_output(opts[:output]) do |out, out_type|
    each_scan(:ms_level => opts[:ms_levels]) do |scan|
      sn = scan.num

      next unless included_scans[sn] if included_scans
      next unless scan.num_peaks >= opts[:min_peaks]
      
      opts, chrg_sts, pmz = get_vals(opts, scan)
      
      chrg_sts.each do |z|
        mh = (pmz * z) - (z - 1)*Ms::Mass::PROTON
        next unless (mh >= opts[:bottom_mh]) 
        next unless (mh <= opts[:top_mh]) if opts[:top_mh]
        
        case format
        when :mgf ; mgf_header(out, scan, sn, z, mgf_prec_string, pmz, (retention_times ? scan.time : nil))
        when :ms2 ; ms2_header(out, scan, sn, z, mh, pmz)
        end
        
        scan.spectrum.peaks do |mz,int|
          unless opts[:filter_zero_intensity] && (int == 0.0)
            out.printf(frag_string, mz, sep, int)
          end
        end
        
        out.puts "END IONS\n\n" if format == :mgf
      end
    end
    
    if out_type == :string_io
      out.string
    else
      count
    end
  end
end