ms-sequest 0.1.2 → 0.2.1

data/lib/ms/sequest/srf.rb

@@ -11,16 +11,14 @@ require 'ms/ident/protein'
 require 'ms/sequest/params'
 
 
-module Ms ; end
-module Ms::Sequest ; end
-
-class Ms::Sequest::Srf < Ms::Ident::Search
+module MS ; end
+module MS::Sequest ; end
 
+class MS::Sequest::Srf < MS::Ident::Search
   class NoSequestParamsError < ArgumentError
   end
 
-
-  # inherits peptides and proteins from Search
+  # inherits peptide_hits from Search
 
   # a String: 3.5, 3.3 or 3.2
   attr_accessor :version
@@ -48,7 +46,7 @@ class Ms::Sequest::Srf < Ms::Ident::Search
   attr_accessor :filtered_by_precursor_mass_tolerance 
 
   def protein_class
-    Ms::Sequest::Srf::Out::Protein
+    MS::Sequest::Srf::Out::Protein
   end
 
   # returns a Sequest::Params object or nil if none
@@ -65,7 +63,7 @@ class Ms::Sequest::Srf < Ms::Ident::Search
       if sequest_start_from_last_half = last_half.rindex('[SEQUEST]')
         params_start_index =  sequest_start_from_last_half + halfway
         handle.seek(params_start_index)
-        params = Ms::Sequest::Params.new.parse_io(handle)
+        params = MS::Sequest::Params.new.parse_io(handle)
         finish_parsing_io_pos = handle.pos
       else
         nil  # not found
@@ -85,24 +83,14 @@ class Ms::Sequest::Srf < Ms::Ident::Search
   
   # opts:
   #     :filter_by_precursor_mass_tolerance => true | false (default true)
-  #     # this will filter by the sequest params prec tolerance as is
-  #     # typically done by Bioworks.
-  #
-  #     :link_protein_hits => true | false (default true)
-  #     # if true, generates the @protein attribute for the :protein method
-  #     #   and creates one protein per reference that is linked to each 
-  #     #   relevant peptide hit.
-  #     # if false, each protein for each peptide hit is a unique object 
-  #     # and the :proteins method returns nil.  If you are merging multiple
-  #     # searches then you probably want to set this to false to avoid
-  #     # recalculation.
+  #          this will filter by the sequest params prec tolerance as is
+  #          typically done by the Bioworks software.
   #
   #     :read_pephits => true | false (default true)
-  #     # will attempt to read peptide hit information (equivalent to .out
-  #     # files), otherwise, just reads the dta information.
+  #          will attempt to read peptide hit information (equivalent to .out
+  #          files), otherwise, just reads the dta information.
   def initialize(filename=nil, opts={})
     @peptide_hits = []
-
     @dta_files = []
     @out_files = []
     if filename
@@ -111,12 +99,12 @@ class Ms::Sequest::Srf < Ms::Ident::Search
   end
 
 
-  # 1. updates the out_file's list of hits based on passing peptides (but not
+  # 1. updates the out_file's list of hits based on passing peptide_hits (but not
   # the original hit id; rank is implicit in array ordering)
   # 2. recalculates deltacn values completely if number of hits changed (does
   # not touch deltacn orig)
   #
-  # This can spoil proper protein -> peptide linkages.  Ms::Id::Search.merge!
+  # This can spoil proper protein -> peptide linkages.  MS::Id::Search.merge!
   # should be run after this method to ensure correct protein -> peptide
   # linkages.
   def filter_by_precursor_mass_tolerance!
@@ -151,7 +139,7 @@ class Ms::Sequest::Srf < Ms::Ident::Search
       end
       if hits.size != before
         out_file.hits = hits # <- is this necessary 
-        Ms::Sequest::Srf::Out::Peptide.update_deltacns_from_xcorr(hits)
+        MS::Sequest::Srf::Out::Peptide.update_deltacns_from_xcorr(hits)
         out_file.num_hits = hits.size
       end
     end
@@ -165,9 +153,9 @@ class Ms::Sequest::Srf < Ms::Ident::Search
     fh.pos = start
 
     num_files.times do |i|
-      dta_files[i] = Ms::Sequest::Srf::Dta.from_io(fh, unpack_35) 
+      dta_files[i] = MS::Sequest::Srf::Dta.from_io(fh, unpack_35) 
       #p dta_files[i]
-      out_files[i] = Ms::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
+      out_files[i] = MS::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
       #p out_files[i]
     end
     [dta_files, out_files]
@@ -177,9 +165,9 @@ class Ms::Sequest::Srf < Ms::Ident::Search
   # opts are the same as for 'new'
   def from_file(filename, opts)
     @resident_dir = File.dirname(File.expand_path(filename))
-    opts = { :filter_by_precursor_mass_tolerance => true, :link_protein_hits => true, :read_pephits => true}.merge(opts)
+    opts = { :filter_by_precursor_mass_tolerance => true, :read_pephits => true}.merge(opts)
 
-    (@params, after_params_io_pos) = Ms::Sequest::Srf.get_sequest_params_and_finish_pos(filename)
+    (@params, after_params_io_pos) = MS::Sequest::Srf.get_sequest_params_and_finish_pos(filename)
     return unless @params
 
     dup_references = 0
@@ -204,7 +192,7 @@ class Ms::Sequest::Srf < Ms::Ident::Search
     end
 
     File.open(filename, 'rb') do |fh|
-      @header = Ms::Sequest::Srf::Header.from_io(fh)
+      @header = MS::Sequest::Srf::Header.from_io(fh)
       @version = @header.version
 
       unpack_35 = case @version
@@ -283,13 +271,6 @@ class Ms::Sequest::Srf < Ms::Ident::Search
       end
 
       filter_by_precursor_mass_tolerance! if params
-
-      if opts[:link_protein_hits]
-        (@peptide_hits, @proteins) = merge!([self.peptide_hits]) do |_protein, _peptides|
-          Ms::Sequest::Srf::Out::Protein.new(_protein.reference, _peptides)
-        end
-      end
-
     end
 
     self
@@ -323,7 +304,7 @@ class Ms::Sequest::Srf < Ms::Ident::Search
     fh.pos = start
 
     header.num_dta_files.times do |i|
-      dta_files[i] = Ms::Sequest::Srf::Dta.from_io(fh, unpack_35) 
+      dta_files[i] = MS::Sequest::Srf::Dta.from_io(fh, unpack_35) 
     end
     dta_files
   end
@@ -333,14 +314,14 @@ class Ms::Sequest::Srf < Ms::Ident::Search
   def read_out_files(fh,number_files, unpack_35, dup_refs_gt_0)
     out_files = Array.new(number_files)
     header.num_dta_files.times do |i|
-      out_files[i] = Ms::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
+      out_files[i] = MS::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
     end
     out_files
   end
 
 end
 
-class Ms::Sequest::Srf::Header
+class MS::Sequest::Srf::Header
 
   Start_byte = {
     :enzyme => 438,
@@ -369,7 +350,7 @@ class Ms::Sequest::Srf::Header
   }
 
   attr_accessor :version
-  # a Ms::Sequest::Srf::DtaGen object
+  # a MS::Sequest::Srf::DtaGen object
   attr_accessor :dta_gen
   attr_accessor :enzyme
   attr_accessor :ion_series
@@ -401,7 +382,7 @@ class Ms::Sequest::Srf::Header
   def from_io(fh)
     st = fh.read(4) 
     @version = '3.' + st.unpack('I').first.to_s
-    @dta_gen = Ms::Sequest::Srf::DtaGen.from_io(fh)
+    @dta_gen = MS::Sequest::Srf::DtaGen.from_io(fh)
     # if the start_mass end_mass start_scan and end_scan are all zero, its a
     # combined srf file:
     @combined = [0.0, 0.0, 0, 0].zip(%w(start_mass end_mass start_scan end_scan)).all? do |one,two|
@@ -438,7 +419,7 @@ class Ms::Sequest::Srf::Header
 end
 
 # the Dta Generation Params
-class Ms::Sequest::Srf::DtaGen
+class MS::Sequest::Srf::DtaGen
 
   ## not sure if this is correct
   # Float
@@ -479,9 +460,9 @@ end
 # total_num_possible_charge_states is not correct under 3.5 (Bioworks 3.3.1)
 # unknown is, well unknown...
 
-Ms::Sequest::Srf::Dta = Struct.new( *%w(mh dta_tic num_peaks charge ms_level unknown total_num_possible_charge_states peaks).map(&:to_sym) )
+MS::Sequest::Srf::Dta = Struct.new( *%w(mh dta_tic num_peaks charge ms_level unknown total_num_possible_charge_states peaks).map(&:to_sym) )
 
-class Ms::Sequest::Srf::Dta 
+class MS::Sequest::Srf::Dta 
   # original
   # Unpack = "EeIvvvv"
   Unpack_32 = "EeIvvvv"
@@ -496,7 +477,7 @@ class Ms::Sequest::Srf::Dta
   def inspect
     peaks_st = 'nil'
     if self[7] ; peaks_st = "[#{self[7].size} bytes]" end
-    "<Ms::Sequest::Srf::Dta @mh=#{mh} @dta_tic=#{dta_tic} @num_peaks=#{num_peaks} @charge=#{charge} @ms_level=#{ms_level} @total_num_possible_charge_states=#{total_num_possible_charge_states} @peaks=#{peaks_st} >"
+    "<MS::Sequest::Srf::Dta @mh=#{mh} @dta_tic=#{dta_tic} @num_peaks=#{num_peaks} @charge=#{charge} @ms_level=#{ms_level} @total_num_possible_charge_states=#{total_num_possible_charge_states} @peaks=#{peaks_st} >"
   end
 
   def self.from_io(fh, unpack_35)
@@ -543,12 +524,12 @@ class Ms::Sequest::Srf::Dta
 end
 
 
-#Ms::Sequest::Srf::Out = Struct.new( *%w(first_scan last_scan charge num_hits computer date_time hits total_inten lowest_sp num_matched_peptides db_locus_count).map(&:to_sym) )
-Ms::Sequest::Srf::Out = Struct.new( *%w(num_hits computer date_time total_inten lowest_sp num_matched_peptides db_locus_count hits first_scan last_scan charge).map(&:to_sym) )
+#MS::Sequest::Srf::Out = Struct.new( *%w(first_scan last_scan charge num_hits computer date_time hits total_inten lowest_sp num_matched_peptides db_locus_count).map(&:to_sym) )
+MS::Sequest::Srf::Out = Struct.new( *%w(num_hits computer date_time total_inten lowest_sp num_matched_peptides db_locus_count hits first_scan last_scan charge).map(&:to_sym) )
 
 # 0=first_scan, 1=last_scan, 2=charge, 3=num_hits, 4=computer, 5=date_time, 6=hits, 7=total_inten, 8=lowest_sp, 9=num_matched_peptides, 10=db_locus_count
 
-class Ms::Sequest::Srf::Out
+class MS::Sequest::Srf::Out
   Unpack_32 = '@36vx2Z*@60Z*'
   Unpack_35 = '@36vx4Z*@62Z*'
 
@@ -560,10 +541,10 @@ class Ms::Sequest::Srf::Out
       else
         ''
       end
-    "<Ms::Sequest::Srf::Out  first_scan=#{first_scan}, last_scan=#{last_scan}, charge=#{charge}, num_hits=#{num_hits}, computer=#{computer}, date_time=#{date_time}#{hits_s}>"
+    "<MS::Sequest::Srf::Out  first_scan=#{first_scan}, last_scan=#{last_scan}, charge=#{charge}, num_hits=#{num_hits}, computer=#{computer}, date_time=#{date_time}#{hits_s}>"
   end
 
-  # returns an Ms::Sequest::Srf::Out object
+  # returns an MS::Sequest::Srf::Out object
   def self.from_io(fh, unpack_35, dup_refs_gt_0)
     ## EMPTY out file is 96 bytes
     ## each hit is 320 bytes
@@ -582,16 +563,16 @@ class Ms::Sequest::Srf::Out
     if ar.size > 0
       num_extra_references = 0
       _num_hits.times do |i|
-        ar[i] = Ms::Sequest::Srf::Out::Peptide.from_io(fh, unpack_35)
+        ar[i] = MS::Sequest::Srf::Out::Peptide.from_io(fh, unpack_35)
         num_extra_references += ar[i].num_other_loci
       end
       if dup_refs_gt_0
-        Ms::Sequest::Srf::Out::Peptide.read_extra_references(fh, num_extra_references, ar)
+        MS::Sequest::Srf::Out::Peptide.read_extra_references(fh, num_extra_references, ar)
       end
       ## The xcorrs are already ordered by best to worst hit
       ## ADJUST the deltacn's to be meaningful for the top hit:
       ## (the same as bioworks and prophet)
-      Ms::Sequest::Srf::Out::Peptide.set_deltacn_from_deltacn_orig(ar)
+      MS::Sequest::Srf::Out::Peptide.set_deltacn_from_deltacn_orig(ar)
     end
     out_obj.hits = ar
     out_obj[1].chomp! # computer
@@ -620,10 +601,10 @@ end
 # num_other_loci is the number of other loci that the peptide matches beyond
 # the first one listed
 # srf = the srf object this scan came from
-Ms::Sequest::Srf::Out::Peptide = Struct.new( *%w(mh deltacn_orig sf sp xcorr id num_other_loci rsp ions_matched ions_total sequence proteins deltamass ppm aaseq base_name first_scan last_scan charge srf deltacn deltacn_orig_updated).map(&:to_sym) )
+MS::Sequest::Srf::Out::Peptide = Struct.new( *%w(mh deltacn_orig sf sp xcorr id num_other_loci rsp ions_matched ions_total sequence proteins deltamass ppm aaseq base_name first_scan last_scan charge srf deltacn deltacn_orig_updated).map(&:to_sym) )
 # 0=mh 1=deltacn_orig 2=sp 3=xcorr 4=id 5=num_other_loci 6=rsp 7=ions_matched 8=ions_total 9=sequence 10=proteins 11=deltamass 12=ppm 13=aaseq 14=base_name 15=first_scan 16=last_scan 17=charge 18=srf 19=deltacn 20=deltacn_orig_updated
 
-class Ms::Sequest::Srf::Out::Peptide
+class MS::Sequest::Srf::Out::Peptide
 
   # creates the deltacn that is meaningful for the top hit (the deltacn_orig
   # or the second best hit and so on).
@@ -656,7 +637,7 @@ class Ms::Sequest::Srf::Out::Peptide
       pep = pep_hits[fh.read(8).unpack('x4I').first - 1]
 
       ref = fh.read(80).unpack('A*').first
-      pep[11] << Ms::Sequest::Srf::Out::Protein.new(ref[0,38])
+      pep[11] << MS::Sequest::Srf::Out::Protein.new(ref[0,38])
     end
     #  fh.read(6) if unpack_35
   end
@@ -695,9 +676,9 @@ class Ms::Sequest::Srf::Out::Peptide
     end
     st.push('>')
     st.join(' ')
-    #"<Ms::Sequest::Srf::Out::Peptide @mh=#{mh}, @deltacn=#{deltacn}, @sp=#{sp}, @xcorr=#{xcorr}, @id=#{id}, @rsp=#{rsp}, @ions_matched=#{ions_matched}, @ions_total=#{ions_total}, @sequence=#{sequence}, @proteins(count)=#{proteins.size}, @deltamass=#{deltamass}, @ppm=#{ppm} @aaseq=#{aaseq}, @base_name=#{base_name}, @first_scan=#{first_scan}, @last_scan=#{last_scan}, @charge=#{charge}, @srf(base_name)=#{srf.base_name}>"
+    #"<MS::Sequest::Srf::Out::Peptide @mh=#{mh}, @deltacn=#{deltacn}, @sp=#{sp}, @xcorr=#{xcorr}, @id=#{id}, @rsp=#{rsp}, @ions_matched=#{ions_matched}, @ions_total=#{ions_total}, @sequence=#{sequence}, @proteins(count)=#{proteins.size}, @deltamass=#{deltamass}, @ppm=#{ppm} @aaseq=#{aaseq}, @base_name=#{base_name}, @first_scan=#{first_scan}, @last_scan=#{last_scan}, @charge=#{charge}, @srf(base_name)=#{srf.base_name}>"
   end
-  # extra_references_array is an array that grows with peptides as extra
+  # extra_references_array is an array that grows with peptide_hits as extra
   # references are discovered.
   def self.from_io(fh, unpack_35)
     ## get the first part of the info
@@ -712,9 +693,9 @@ class Ms::Sequest::Srf::Out::Peptide
 
     # we are slicing the reference to 38 chars to be the same length as
     # duplicate references
-    peptide[11] = [Ms::Sequest::Srf::Out::Protein.new(peptide[11][0,38])]
+    peptide[11] = [MS::Sequest::Srf::Out::Protein.new(peptide[11][0,38])]
 
-    peptide[14] = Ms::Ident::Peptide.sequence_to_aaseq(peptide[10])
+    peptide[14] = MS::Ident::Peptide.sequence_to_aaseq(peptide[10])
 
     fh.read(6) if unpack_35
 
@@ -723,81 +704,12 @@ class Ms::Sequest::Srf::Out::Peptide
 
 end
 
+class MS::Sequest::Srf::Out::Protein < MS::Ident::Protein
+  alias_method :reference, :id
 
-Ms::Sequest::Srf::Out::Protein = Struct.new( *%w(reference peptides).map(&:to_sym) )
-
-class Ms::Sequest::Srf::Out::Protein
-  #include Ms::Ident::Protein
-
-  ## we shouldn't have to do this because this is inlcuded in SpecID::Protein, but
-  ## under some circumstances it won't work without explicitly calling it.
-  #include ProteinReferenceable 
-
-  tmp = $VERBOSE ; $VERBOSE = nil
-  def initialize(reference=nil, peptides=[])
-    self[0] = reference
-    self[1] = peptides
-  end
-  $VERBOSE = tmp
-
+  # the first entry
   def first_entry
-    reference.split(/[\s\r]/)[0]
-  end
-
-  #  "<Ms::Sequest::Srf::Out::Protein reference=\"#{@reference}\">"
-
-  undef_method :inspect
-  def inspect
-    "<Ms::Sequest::Srf::Out::Protein @reference=#{reference}, @peptides(#)=#{peptides.size}>"
-  end
-end
-
-class Ms::Sequest::SrfGroup 
-  include Ms::Ident::SearchGroup
-
-  # inherits an array of Ms::Sequest::Srf::Out::Peptide objects
-  # inherits an array of Ms::Sequest::Srf::Out::Protein objects
-
-  # see Ms::Id::Search for acceptable arguments
-  # (filename, filenames, array of objects)
-  # opts = 
-  #     :filter_by_precursor_mass_tolerance => true | false (default true)
-  def initialize(arg, opts={}, &block)
-    orig_opts = opts.dup
-    indiv_opts = { :link_protein_hits => false }
-    super(arg, opts.merge(indiv_opts)) do
-      unless orig_opts[:link_protein_hits] == false
-        (@peptides, @proteins) = merge!(@searches.map {|v| v.peptides }) do |_prot, _peps|
-          Ms::Sequest::Srf::Out::Protein.new(_prot.reference, _peps)
-        end
-      end
-    end
-    block.call(self) if block_given?
-  end
-
-  def search_class
-    Ms::Sequest::Srf
-  end
-
-  # returns the filename used
-  # if the file exists, the name will be expanded to full path, otherwise just
-  # what is given
-  def to_srg(srg_filename='bioworks.srg')
-    File.open(srg_filename, 'w') do |v|
-      @filenames.each do |srf_file|
-        if File.exist? srf_file
-          v.puts File.expand_path(srf_file)
-        else
-          v.puts srf_file
-        end
-      end
-    end
-    srg_filename
+    reference.split(' ',2)[0]
   end
 end
 
-
-
-
-
-

data/lib/ms/sequest/srf/pepxml.rb

@@ -6,7 +6,7 @@ require 'ms/ident/pepxml/search_hit'
 require 'ms/sequest/srf'
 require 'ms/sequest/pepxml'
 
-class Ms::Sequest::Srf
+class MS::Sequest::Srf
   module Pepxml
 
     #  A hash with the following *symbol* keys may be set:
@@ -36,7 +36,7 @@ class Ms::Sequest::Srf
     # *:retention_times*:: false - <i>include retention times in the file (requires mz_dir to be set)</i>
     # *:deltacn_orig*:: false - <i>when true, the original SEQUEST deltacn values are used.  If false, Bioworks deltacn values are used which are derived by taking the original deltacn of the following hit.  This gives the top ranking hit an informative deltacn but makes the deltacn meaningless for other hits.</i>
     #
-    # *:pepxml_version*:: Ms::Ident::Pepxml::DEFAULT_PEPXML_VERSION, - <i>Integer to set the pepxml version.  The converter and xml output attempts to produce xml specific to the version.</i>
+    # *:pepxml_version*:: MS::Ident::Pepxml::DEFAULT_PEPXML_VERSION, - <i>Integer to set the pepxml version.  The converter and xml output attempts to produce xml specific to the version.</i>
     # *:verbose*:: true - <i>set to false to quiet warnings</i>
     DEFAULT_OPTIONS = {
       :ms_model => nil,
@@ -61,7 +61,7 @@ class Ms::Sequest::Srf
       :retention_times => false,
       :deltacn_orig => false,
 
-      :pepxml_version => Ms::Ident::Pepxml::DEFAULT_PEPXML_VERSION,
+      :pepxml_version => MS::Ident::Pepxml::DEFAULT_PEPXML_VERSION,
       :verbose => true,
     }
 
@@ -80,7 +80,7 @@ class Ms::Sequest::Srf
       [/\w+/, 'UNKNOWN'],
     ]
 
-    # returns an Ms::Ident::Pepxml object.  See that object for creating an
+    # returns an MS::Ident::Pepxml object.  See that object for creating an
     # xml string or writing to file.
     def to_pepxml(opts={})
       opt = DEFAULT_OPTIONS.merge(opts)
@@ -126,7 +126,7 @@ class Ms::Sequest::Srf
         puts msg.join("\n") if opt[:verbose]
       end
 
-      modifications_obj = Ms::Sequest::Pepxml::Modifications.new(params, srf.header.modifications)
+      modifications_obj = MS::Sequest::Pepxml::Modifications.new(params, srf.header.modifications)
       mass_index = params.mass_index(:precursor)
       h_plus = mass_index['h+']
 
@@ -141,7 +141,7 @@ class Ms::Sequest::Srf
           raise NotImplementedError, "will implement shortly"
           #mz_file = Dir[File.join(opt[:mz_dir], srf.base_name_noext + opt[:raw_data].first)].first
           #if mz_file
-          #  Ms::Msrun.scans_to_times(mz_file) 
+          #  MS::Msrun.scans_to_times(mz_file) 
           #else
           #  warn "turning retention_times off since no valid mz[X]ML file was found!!!"
           #  opt[:retention_times] = false
@@ -151,28 +151,28 @@ class Ms::Sequest::Srf
 
       summary_xml_filename = srf.base_name_noext + '.xml'
 
-      pepxml = Ms::Ident::Pepxml.new do |msms_pipeline_analysis|
+      pepxml = MS::Ident::Pepxml.new do |msms_pipeline_analysis|
         msms_pipeline_analysis.merge!(:summary_xml => summary_xml_filename, :pepxml_version => opt[:pepxml_version]) do |msms_run_summary|
           # prep the sample enzyme and search_summary
           msms_run_summary.merge!(
-            { :base_name => File.join(opt[:mz_dir], srf.base_name_noext),
+            :base_name => File.join(opt[:mz_dir], srf.base_name_noext),
             :ms_manufacturer => opt[:ms_manufacturer],
             :ms_model => opt[:ms_model],
             :ms_ionization => opt[:ms_ionization],
             :ms_mass_analyzer => opt[:ms_mass_analyzer],
             :ms_detector => opt[:ms_detector],
             :raw_data => opt[:raw_data].first,
-            :raw_data_type => opt[:raw_data].first, }
+            :raw_data_type => opt[:raw_data].first,
           ) do |sample_enzyme, search_summary, spectrum_queries|
             sample_enzyme.merge!(params.sample_enzyme_hash)
             sample_enzyme.name = opt[:enzyme] if opt[:enzyme]
             search_summary.merge!(
-              { :base_name=> srf.resident_dir + '/' + srf.base_name_noext,
+              :base_name=> srf.resident_dir + '/' + srf.base_name_noext,
               :search_engine => 'SEQUEST',
               :precursor_mass_type => params.precursor_mass_type,
               :fragment_mass_type => params.fragment_mass_type,
               :out_data_type => opt[:out_data_type],
-              :out_data => opt[:out_data], }
+              :out_data => opt[:out_data],
             ) do |search_database, enzymatic_search_constraint, modifications_ar, parameters_hash|
               search_database.merge!(:local_path => db_filename, :seq_type => opt[:db_seq_type], :database_name => opt[:db_name], :orig_database_url => opt[:db_orig_url], :database_release_date => opt[:db_release_date], :database_release_identifier => opt[:db_release_id])
 
@@ -184,9 +184,9 @@ class Ms::Sequest::Srf
               end
 
               enzymatic_search_constraint.merge!(
-                { :enzyme => opt[:enzyme] ? opt[:enzyme] : params.enzyme, 
+                :enzyme => opt[:enzyme] ? opt[:enzyme] : params.enzyme, 
                 :max_num_internal_cleavages => params.max_num_internal_cleavages,
-                :min_number_termini => params.min_number_termini, }
+                :min_number_termini => params.min_number_termini,
               )
               modifications_ar.replace(modifications_obj.modifications)
               parameters_hash.merge!(params.opts)
@@ -196,9 +196,9 @@ class Ms::Sequest::Srf
               precursor_neutral_mass = dta_file.mh - h_plus
 
               search_hits = out_file.hits[0,opt[:num_hits]].each_with_index.map do |pep,i|
-                (prev_aa, pure_aaseq, next_aa) = Ms::Ident::Peptide.prepare_sequence(pep.sequence)
+                (prev_aa, pure_aaseq, next_aa) = MS::Ident::Peptide.prepare_sequence(pep.sequence)
                 calc_neutral_pep_mass = pep.mh - h_plus
-                sh = Ms::Ident::Pepxml::SearchHit.new(
+                sh = MS::Ident::Pepxml::SearchHit.new(
                   :hit_rank => i+1, 
                   :peptide => pure_aaseq, 
                   :peptide_prev_aa => prev_aa,
@@ -211,7 +211,7 @@ class Ms::Sequest::Srf
                   :massdiff => precursor_neutral_mass - calc_neutral_pep_mass,
                   :num_tol_term => sample_enzyme.num_tol_term(prev_aa, pure_aaseq, next_aa),
                   :num_missed_cleavages => sample_enzyme.num_missed_cleavages(pure_aaseq),
-                  :modification_info => modifications_obj.modification_info(Ms::Ident::Peptide.split_sequence(pep.sequence)[1])
+                  :modification_info => modifications_obj.modification_info(MS::Ident::Peptide.split_sequence(pep.sequence)[1])
                 ) do |search_scores|
                   if opt[:deltacn_orig]
                     deltacn = pep.deltacn_orig
@@ -227,7 +227,7 @@ class Ms::Sequest::Srf
                 end
               end
 
-              sr = Ms::Ident::Pepxml::SearchResult.new(:search_hits => search_hits)
+              sr = MS::Ident::Pepxml::SearchResult.new(:search_hits => search_hits)
 
               ret_time = 
                 if opt[:retention_times]
@@ -239,11 +239,11 @@ class Ms::Sequest::Srf
                     times.inject(&:+) / times.size.to_f
                   end
                 end
-              Ms::Ident::Pepxml::SpectrumQuery.new(
-                { :spectrum  => [srf.base_name_noext, *i_ar].join('.'), :start_scan => i_ar[0], :end_scan => i_ar[1], 
+              MS::Ident::Pepxml::SpectrumQuery.new(
+                :spectrum  => [srf.base_name_noext, *i_ar].join('.'), :start_scan => i_ar[0], :end_scan => i_ar[1], 
                 :precursor_neutral_mass => dta_file.mh - h_plus, :assumed_charge => i_ar[2],
                 :retention_time_sec => ret_time,  
-                :search_results => [sr], }
+                :search_results => [sr], 
               )
             end
             spectrum_queries.replace(spec_queries)
@@ -259,7 +259,7 @@ end # Srf
 
 require 'trollop'
 
-module Ms::Sequest::Srf::Pepxml
+module MS::Sequest::Srf::Pepxml
   def self.commandline(argv, progname=$0)
     opts = Trollop::Parser.new do
       banner %Q{
@@ -281,7 +281,7 @@ module Ms::Sequest::Srf::Pepxml
 
       text ""
       text "minor options:"
-      opt :pepxml_version, 'schema version number to use', :default => Ms::Ident::Pepxml::DEFAULT_PEPXML_VERSION
+      opt :pepxml_version, 'schema version number to use', :default => MS::Ident::Pepxml::DEFAULT_PEPXML_VERSION
       opt :ms_model, 'mass spectrometer model', :type => :string
       opt :ms_ionization, 'type of ms ionization', :default => 'ESI'
       opt :ms_detector, 'ms detector', :default => 'UNKNOWN'
@@ -307,7 +307,7 @@ module Ms::Sequest::Srf::Pepxml
 
     argv.zip(opt.delete(:outdirs)) do |srf_file,outdir|
       outdir ||= File.dirname(srf_file)
-      srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
+      srf = MS::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
       pepxml = srf.to_pepxml(opt)
       outfile = pepxml.to_xml(outdir)
       puts "wrote file: #{outfile}" if opt[:verbose]