ms-sequest 0.0.11 → 0.0.12

data/lib/ms/sequest/srf.rb

@@ -17,6 +17,7 @@ require 'ms/sequest/params'
 module Ms ; end
 module Ms::Sequest ; end
 
+
 class Ms::Sequest::Srf
 
   class NoSequestParamsError < ArgumentError
@@ -350,8 +351,8 @@ class Ms::Sequest::Srf::Header
     :modifications => 456,
   }
 
-  # a Ms::Sequest::Srf::DTAGen object
   attr_accessor :version
+  # a Ms::Sequest::Srf::DTAGen object
   attr_accessor :dta_gen
   attr_accessor :enzyme
   attr_accessor :ion_series
@@ -732,8 +733,8 @@ end
 class Ms::Sequest::SrfGroup 
   include Ms::Id::SearchGroup
 
-  # inherets an array of Ms::Sequest::Srf::Out::Pep objects
-  # inherets an array of Ms::Sequest::Srf::Out::Prot objects
+  # inherits an array of Ms::Sequest::Srf::Out::Pep objects
+  # inherits an array of Ms::Sequest::Srf::Out::Prot objects
 
   # see Ms::Id::Search for acceptable arguments
   # (filename, filenames, array of objects)

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

@@ -44,7 +44,7 @@ module Ms
       # :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
-      def to_dta_files(out_folder=nil, compress=nil)
+      def to_dta(out_folder=nil, compress=nil)
         outdir = 
           if out_folder ; out_folder
           else base_name

data/lib/ms/sequest/srf/search/tap.rb

@@ -27,7 +27,7 @@ module Ms
           when 'mgf'
             srf.to_mgf(newfile)
           when 'dta'
-            srf.to_dta_files(newfile)
+            srf.to_dta(newfile)
           end
         end
       end

data/script/fasta_ipi_to_ncbi-ish.rb

@@ -0,0 +1,29 @@
+#!/usr/bin/ruby
+
+if ARGV.size == 0
+  puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
+  puts "outputs: <file>_NCBI.fasta ..."
+  puts ""
+  puts "(Bioworks 3.3.1 [maybe others] does not seem to read an IPI"
+  puts "formatted fasta database header lines.  This will change an" 
+  puts "IPI format to an NCBI style format that Bioworks can read."
+  exit
+end
+
+ARGV.each do |file|
+  base = file.chomp(File.extname(file))
+  outfile = base + '_NCBI' + ".fasta"
+  File.open(outfile, 'w') do |out|
+    IO.foreach(file) do |line|
+      if line =~ /^>/
+        (codes, *description) = line[1..-1].split(" ")
+        description = description.join(" ")
+        code_section = codes.split('|').map {|code| (key, val) = code.split(':') ; "#{key}|#{val}|" }.join
+        out.puts ">#{code_section} #{description}"   
+      else
+        out.print line
+      end
+    end
+  end
+end
+

data/spec/ms/sequest/bioworks_spec.rb

@@ -0,0 +1,153 @@
+
+# TODO work on this guy!
+=begin
+
+require File.expand_path( File.dirname(__FILE__) + '/../tap_spec_helper' )
+
+require 'spec_id'
+require 'spec_id/bioworks'
+#require 'benchmark'
+
+describe Bioworks, 'set from an xml file' do
+  # NEED TO DEBUG THIS PROB!
+  it 'can set one with labeled proteins' do
+    file = Tfiles + "/bioworks_with_INV_small.xml"
+    obj = Bioworks.new(file)
+    obj.prots.size.should == 19
+    file = Tfiles + '/bioworks_small.xml'
+    obj = Bioworks.new(file)
+    obj.prots.size.should == 106
+  end
+
+  it 'can parse an xml file NOT derived from multi-concensus' do
+    tf_bioworks_single_xml_small = Tfiles + '/bioworks_single_run_small.xml'
+    obj = Bioworks.new(tf_bioworks_single_xml_small)
+    gfn = '5prot_mix_michrom_20fmol_200pmol'
+    origfilename = '5prot_mix_michrom_20fmol_200pmol.RAW'
+    origfilepath = 'C:\Xcalibur\sequest'
+    obj.global_filename.should == gfn
+    obj.origfilename.should == origfilename
+    obj.origfilepath.should == origfilepath
+    obj.prots.size.should == 7
+    obj.prots.first.peps.first.base_name.should ==  gfn
+    obj.prots.first.peps.first.file.should ==  "152"
+    obj.prots.first.peps.first.charge.should == 2
+    # @TODO: add more tests here
+  end
+
+  it 'can output in excel format (**semi-verified right now)' do
+    tf_bioworks_to_excel = Tfiles + '/tf_bioworks2excel.bioXML'
+    tf_bioworks_to_excel_actual = Tfiles + '/tf_bioworks2excel.txt.actual'
+    tmpfile = Tfiles + "/tf_bioworks_to_excel.tmp"
+    bio = Bioworks.new(tf_bioworks_to_excel)
+    bio.to_excel(tmpfile)
+    tmpfile.exist_as_a_file?.should be_true
+    #File.should exist_as_a_file(tmpfile)
+    exp = _arr_of_arrs(tf_bioworks_to_excel_actual)
+    act = _arr_of_arrs(tmpfile)
+    exp.each_index do |i|
+      break if i == 23 ## this is where the ordering becomes arbitrary between guys with the same scans, but different filenames
+      _assert_equal_pieces(exp[i], act[i], exp[i][0] =~ /\d/)
+    end
+
+    File.unlink tmpfile
+  end
+
+  # prot is boolean if this is a protein line!
+  def _assert_equal_pieces(exp, act, prot)
+    # equal as floats (by delta)
+    exp.each_index do |i|
+      if i == 5  # both prots and peps
+        act[i].to_f.should be_close(exp[i].to_f, 0.1)
+      elsif i == 3 && !prot
+        act[i].to_f.should be_close(exp[i].to_f, 0.01)
+      elsif i == 6 && !prot
+        act[i].to_f.should be_close(exp[i].to_f, 0.01)
+      elsif i == 9 && prot
+        ## NEED TO GET THESE BACK (for consistency):
+        #act[i].split(" ")[0].should =~ exp[i].split(" ")[0]
+      else
+        ## NEED TO GET THESE BACK (for consistency):
+        #act[i].should == exp[i]
+      end
+    end
+  end
+
+  # takes a bioworks excel (in txt format) and outputs an arr of arrs
+  def _arr_of_arrs(file)
+    IO.readlines(file).collect do |line|
+      line.chomp!
+      line.split("\t")
+    end
+  end
+
+  it 'can return unique peptides and proteins by sequence+charge (private)' do
+    cnt = 0
+    answer = [%w(2 PEPTIDE), %w(3 PEPTIDE), %w(3 PEPY), %w(2 PEPY)]
+    exp_peps = answer.collect! do |arr|
+      pep = Bioworks::Pep.new
+      pep.charge = arr[0]
+      pep.sequence = arr[1]
+      pep
+    end
+    exp_prots = [[0,2],[1,4,5],[3],[6]].collect do |arr|
+      arr.collect do |num|
+        prot = Bioworks::Prot.new
+        prot.reference = "#{num}"
+        prot
+      end
+    end
+    exp_peps = exp_peps.zip(exp_prots)
+    exp_peps.collect! do |both|
+      both[0].prots = [both[1]]
+      both[0]
+    end
+
+    peptides = [%w(2 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPTIDE), %w(3 PEPY), %w(3 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPY)].collect do |arr|
+      pep = Bioworks::Pep.new
+      pep.charge = arr[0]
+      pep.sequence = arr[1]
+      pep.prots = [Bioworks::Prot.new]
+      pep.prots.first.reference = "#{cnt}"
+      cnt += 1
+      pep
+    end
+    peptides, proteins = Bioworks.new._uniq_peps_by_sequence_charge(peptides)
+    proteins.size.should == peptides.size
+    exp_peps.each_with_index do |pep, i|
+      peptides[i].charge.should == pep.charge
+      peptides[i].sequence.should == pep.sequence
+    end
+
+    exp_prots.each_index do |i|
+      exp_prots[i].each_index do |j|
+        proteins[i][j].reference.should == exp_prots[i][j].reference
+      end
+    end
+  end
+
+end
+
+describe Bioworks::Pep do
+  it 'can be initialized from a hash' do
+    hash = {:sequence => 0, :mass => 1, :deltamass => 2, :charge => 3, :xcorr => 4, :deltacn => 5, :sp => 6, :rsp => 7, :ions => 8, :count => 9, :tic => 10, :prots => 11, :base_name => 12, :first_scan => 13, :last_scan => 14, :peptide_probability => 15, :file => 16, :_num_prots => 17, :_first_prot => 18}
+    pep = Bioworks::Pep.new(hash)
+    hash.each do |k,v|
+      pep.send(k).should == v
+    end
+  end
+
+  it 'correctly extracts file information' do
+    pep = Bioworks::Pep.new
+    testing = ['005a, 1131', '005b, 1131 - 1133', '1131', '1131 - 1133']
+    answers = [%w(005a 1131 1131), %w(005b 1131 1133), [nil, '1131', '1131'], [nil, '1131', '1133']]
+    testing.zip(answers) do |ar|
+      ans = pep.class.extract_file_info(ar[0])
+      ans.join(" ").should == ar[1].join(" ") 
+    end
+  end
+
+end
+
+
+=end

data/spec/ms/sequest/params_spec.rb

@@ -0,0 +1,131 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+
+require 'ms/sequest/params'
+
+# returns a hash of all params
+def simple_parse(filename)
+  hash = {}
+  IO.read(filename).split(/\r?\n/).select {|v| v =~ /^[a-z]/}.each do |line|
+    if line =~ /([^\s]+)\s*=\s*([^;]+)\s*;?/
+      hash[$1.dup] = $2.rstrip
+    end
+  end
+  hash
+end
+
+shared 'sequest params' do
+  before do
+    @obj = Ms::Sequest::Params.new(@file)
+  end
+
+  it 'has a method for every parameter in the file' do
+    hash = simple_parse(@file)
+    hash.each do |k,v|
+      @obj.send(k.to_sym).is v
+    end
+  end
+
+  it 'returns zero length string for params with no information' do
+    @obj.second_database_name.is ""
+    @obj.sequence_header_filter.is ""
+  end
+
+  it 'returns nil for params that do not exist and have no translation' do
+    @obj.google_plex.is nil
+  end
+
+  it 'provides consistent API between versions for important info' do
+    message = capture_stderr do
+      @api_hash.each do |k,v|
+        @obj.send(k).is v
+      end
+    end
+  end
+
+  it 'provides some backwards compatibility' do
+    @backwards_hash.each do |k,v|
+      @obj.send(k).is v
+    end
+  end
+
+end
+
+describe 'sequest params v 3.1' do
+
+  @file = TESTFILES + '/bioworks31.params'
+  @api_hash = {
+    :version => '3.1',
+    :enzyme => 'Trypsin',
+    :database => "C:\\Xcalibur\\database\\ecoli_K12.fasta",
+    :enzyme_specificity => [1, 'KR', ''],
+    :precursor_mass_type => "average",
+    :fragment_mass_type => "average",
+    :min_number_termini  => '1',
+  }
+
+  @backwards_hash = {
+    :max_num_internal_cleavages => '2',
+    :fragment_ion_tol => '0.0000',
+  }
+
+  behaves_like 'sequest params'
+end
+
+describe 'sequest params v 3.2' do
+  @file = TESTFILES + '/bioworks32.params'
+  @api_hash = {
+    :version => '3.2',
+    :enzyme => 'Trypsin',
+    :database => "C:\\Xcalibur\\database\\ecoli_K12_ncbi_20060321.fasta",
+    :enzyme_specificity => [1, 'KR', 'P'],
+    :precursor_mass_type => "average",
+    :fragment_mass_type => "average",
+    :min_number_termini  => '2',
+  }
+
+  @backwards_hash = {
+    :max_num_internal_cleavages => '2',
+    :fragment_ion_tol => '1.0000',
+  }
+
+  behaves_like 'sequest params'
+end
+
+describe 'sequest params v 3.3' do
+  @file = TESTFILES + '/bioworks33.params'
+  @api_hash = {
+    :version => '3.3',
+    :enzyme => 'Trypsin',
+    :database => "C:\\Xcalibur\\database\\yeast.fasta",
+    :enzyme_specificity => [1, 'KR', ''],
+    :precursor_mass_type => "monoisotopic",
+    :fragment_mass_type => "monoisotopic",
+    :min_number_termini  => '2',
+  }
+
+  @backwards_hash = {
+    :max_num_internal_cleavages => '2',
+    :fragment_ion_tol => '1.0000',
+  }
+  behaves_like 'sequest params'
+end
+
+describe 'sequest params v 3.2 from srf' do
+  @file = TESTFILES + '/7MIX_STD_110802_1.sequest_params_fragment.srf'
+  @api_hash = {
+    :version => '3.2',
+    :enzyme => 'Trypsin',
+    :database => "C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta",
+    :enzyme_specificity => [1, 'KR', 'P'],
+    :precursor_mass_type => "average",
+    :fragment_mass_type => "average",
+    :min_number_termini  => '2',
+  }
+
+  @backwards_hash = {
+    :max_num_internal_cleavages => '2',
+    :fragment_ion_tol => '1.0000',
+  }
+  behaves_like 'sequest params'
+end
+

data/spec/ms/sequest/pepxml_spec.rb

@@ -0,0 +1,376 @@
+
+=begin
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+
+require 'spec_id'
+require 'spec_id/sequest/pepxml'
+#require 'ms/mzxml'
+
+
+NODELETE = false
+
+describe Sequest::PepXML, " created from small bioworks.xml" do
+
+  spec_large do
+    before(:all) do
+      tf_mzxml_path = Tfiles_l + "/yeast_gly_mzXML"
+
+      tf_params = Tfiles + "/bioworks32.params"
+      tf_bioworks_xml = Tfiles + "/bioworks_small.xml"
+      out_path = Tfiles
+      @pepxml_objs = Sequest::PepXML.set_from_bioworks(tf_bioworks_xml, :params => tf_params, :ms_data => tf_mzxml_path, :out_path => out_path)
+    end
+
+    it 'gets some spectrum queries' do
+      @pepxml_objs.each do |obj|
+        (obj.spectrum_queries.size > 2).should be_true
+        (obj.spectrum_queries.first.search_results.first.search_hits.size > 0).should be_true
+      end
+      #@pepxml_objs.each do |pep| puts pep.to_pepxml end
+    end
+  end
+end
+
+
+
+describe Sequest::PepXML, " created from large bioworks.xml" do
+  # assert_equal_by_pairs (really any old array)
+  def assert_equal_pairs(obj, arrs)
+    arrs.each do |arr|
+      #if obj.send(arr[1]) != arr[0]
+      #  puts "HELLO"
+      #  puts "OBJ answer"
+      #  p obj.send(arr[1])
+      #  puts "ar0"
+      #  p arr[0]
+      #  puts "ar1"
+      #  p arr[1]
+      #end
+      if arr[0].is_a? Float
+        obj.send(arr[1]).should be_close(arr[0], 0.0000000001)
+      else
+        obj.send(arr[1]).should == arr[0]
+      end
+    end
+  end
+
+  #swap the first to guys first
+  def assert_equal_pairs_swapped(obj, arrs)
+    arrs.each do |arr|
+      arr[0], arr[1] = arr[1], arr[0] 
+    end
+    assert_equal_pairs(obj, arrs)
+  end
+
+  spec_large do
+    before(:all) do
+      st = Time.new
+      params = Tfiles + "/opd1/sequest.3.2.params"
+      bioworks_xml = Tfiles_l + "/opd1/bioworks.000.oldparams.xml"
+      mzxml_path = Tfiles_l + "/opd1"
+      out_path = Tfiles
+      @pepxml_version = 18
+      @pepxml_objs = Sequest::PepXML.set_from_bioworks_xml(bioworks_xml, params, {:ms_data => mzxml_path, :out_path => out_path, :pepxml_version => @pepxml_version})
+      puts "- takes #{Time.new - st} secs"
+    end
+
+    it 'extracts MSMSPipelineAnalysis' do
+      ######## HMMMMM...
+      Sequest::PepXML.pepxml_version.should == @pepxml_version
+
+      # MSMSPipelineAnalysis
+      po = @pepxml_objs.first
+      msms_pipeline = po.msms_pipeline_analysis
+      msms_pipeline.xmlns.should == 'http://regis-web.systemsbiology.net/pepXML'
+      msms_pipeline.xmlns_xsi.should == 'http://www.w3.org/2001/XMLSchema-instance'
+      msms_pipeline.xsi_schema_location.should == 'http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd'
+      msms_pipeline.summary_xml.should == '000.xml'
+    end
+
+    it 'extracts MSmSRunSummary' do
+      # MSMSRunSummary
+      rs = @pepxml_objs.first.msms_pipeline_analysis.msms_run_summary
+      rs.base_name.should =~ /\/000/
+      assert_equal_pairs(rs, [ ['ThermoFinnigan', :ms_manufacturer], ['LCQ Deca XP Plus', :ms_model], ['ESI', :ms_ionization], ['Ion Trap', :ms_mass_analyzer], ['UNKNOWN', :ms_detector], ['raw', :raw_data_type], ['.mzXML', :raw_data], ])
+    end
+
+    it 'extracts SampleEnzyme' do
+      # SampleEnzyme
+      se = @pepxml_objs.first.msms_pipeline_analysis.msms_run_summary.sample_enzyme
+      assert_equal_pairs(se, [ ['Trypsin', :name], ['KR', :cut], [nil, :no_cut], ['C', :sense], ])
+    end
+
+    it 'extracts SearchSummary' do
+      # SearchSummary
+      ss = @pepxml_objs.first.msms_pipeline_analysis.msms_run_summary.search_summary
+      ss.is_a?(Sequest::PepXML::SearchSummary).should be_true
+      ss.base_name.should =~ /\/000/
+      ss.peptide_mass_tol.should =~ /1\.500/
+      assert_equal_pairs_swapped(ss, [ # normal attributes
+                                 [:search_engine, "SEQUEST"], [:precursor_mass_type, "average"], [:fragment_mass_type, "average"], [:out_data_type, "out"], [:out_data, ".tgz"], [:search_id, "1"],
+
+                                 # enzymatic_search_constraint
+                                 [:enzyme, 'Trypsin'], [:max_num_internal_cleavages, '2'], [:min_number_termini, '2'],
+
+                                 # parameters
+                                 [:fragment_ion_tol, "1.0000"], [:ion_series, "0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"], [:max_num_differential_AA_per_mod, "3"], [:nucleotide_reading_frame, "0"], [:num_output_lines, "10"], [:remove_precursor_peak, "0"], [:ion_cutoff_percentage, "0.0000"], [:match_peak_count, "0"], [:match_peak_allowed_error, "1"], [:match_peak_tolerance, "1.0000"], [:protein_mass_filter, "0 0"],
+      ])
+
+    end
+    it 'extracts SearchDatabase' do
+      # SearchDatabase
+      sd = @pepxml_objs.first.msms_pipeline_analysis.msms_run_summary.search_summary.search_database
+      sd.is_a?(Sequest::PepXML::SearchDatabase).should be_true
+      assert_equal_pairs_swapped(sd, [ [:local_path, "C:\\Xcalibur\\database\\ecoli_K12.fasta"], [:seq_type, 'AA'], ])
+    end
+
+    it 'returns SpectrumQueries' do
+      # SpectrumQueries
+      sq = @pepxml_objs.first.msms_pipeline_analysis.msms_run_summary.spectrum_queries
+      spec = sq.first 
+      assert_equal_pairs_swapped(spec, [
+                                 [:spectrum, "000.100.100.1"], [:start_scan, "100"], [:end_scan, "100"],
+                                 #[:precursor_neutral_mass, "1074.5920"], # out2summary
+                                 [:precursor_neutral_mass, 1074.666926], # mine
+                                 [:assumed_charge, 1], [:index, "1"],
+      ])
+      sh = spec.search_results.first.search_hits.first
+      assert_equal_pairs_swapped(sh, [
+                                 # normal attributes
+                                 [:hit_rank, 1], 
+                                 [:peptide, "SIYFRNFK"], 
+                                 [:peptide_prev_aa, "R"], 
+                                 [:peptide_next_aa, "G"], 
+                                 [:protein, "gi|16130084|ref|NP_416651.1|"], 
+                                 [:num_tot_proteins, 1], 
+                                 [:num_matched_ions, 4], 
+                                 [:tot_num_ions, 14],
+                                 #[:calc_neutral_pep_mass, "1074.1920"], # out2summary
+                                 [:calc_neutral_pep_mass, 1074.23261], # mine
+                                 #[:massdiff, "+0.400000"], # out2summary
+                                 [:massdiff, 0.434316000000081],  # mine
+                                 [:num_tol_term, 2], [:num_missed_cleavages, 1], [:is_rejected, 0],
+
+                                 # search_score
+                                 [:xcorr, 0.4], [:deltacn, 0.023], [:deltacnstar, "0"], [:spscore, 78.8], [:sprank, 1],
+      ])
+
+      spec = sq[1]
+      assert_equal_pairs_swapped(spec, [
+                                 [:spectrum, "000.1000.1000.1"], [:start_scan, "1000"], [:end_scan, "1000"], #[:precursor_neutral_mass, "663.1920"], # out2summary
+                                 [:precursor_neutral_mass, 663.206111], # mine
+                                 [:assumed_charge, 1], [:index, "2"],
+      ])
+
+      sh = spec.search_results.first.search_hits.first
+      assert_equal_pairs_swapped(sh, [
+                                 # normal attributes
+                                 [:hit_rank, 1], [:peptide, "ALADFK"], [:peptide_prev_aa, "R"], [:peptide_next_aa, "S"], [:protein, "gi|16128765|ref|NP_415318.1|"], [:num_tot_proteins, 1], [:num_matched_ions, 5], [:tot_num_ions, 10],
+                                 [:num_tol_term, 2], [:num_missed_cleavages, 0], [:is_rejected, 0],
+                                 #[:massdiff, "-0.600000"], # out2summary
+                                 [:massdiff, -0.556499000000031],  # mine
+                                 #[:calc_neutral_pep_mass, 663.7920], # out2summary
+                                 [:calc_neutral_pep_mass, 663.76261], # mine
+
+                                 # search_score
+                                 [:xcorr, 0.965], [:deltacn, 0.132], [:deltacnstar, "0"], [:spscore, 81.1], [:sprank, 1],
+      ])
+
+      spec = sq[9]
+      assert_equal_pairs_swapped(spec, [
+                                 [:spectrum, "000.1008.1008.2"], [:start_scan, "1008"], [:end_scan, "1008"], [:assumed_charge, 2],
+                                 #[:precursor_neutral_mass, "691.0920"], # out2summary
+                                 [:precursor_neutral_mass, 691.150992], # mine
+      ])
+
+      sh = spec.search_results.first.search_hits.first
+      assert_equal_pairs_swapped(sh, [
+                                 # normal attributes
+                                 [:hit_rank, 1], [:peptide, "RLFTR"], [:peptide_prev_aa, "R"], [:peptide_next_aa, "A"], [:protein, "gi|16130457|ref|NP_417027.1|"], [:num_tot_proteins, 1], [:num_matched_ions, 5], [:tot_num_ions, 8], [:num_tol_term, 2], 
+
+                                 #[:num_missed_cleavages, "0"],  # out2summary misses this!
+                                 [:num_missed_cleavages, 1], 
+                                 [:is_rejected, 0],
+                                 #[:calc_neutral_pep_mass, "691.7920"], # out2summary
+                                 [:calc_neutral_pep_mass, 691.82261], # mine
+                                 #[:massdiff, "-0.700000"], # out2summary
+                                 [:massdiff, -0.67161800000008],  # mine
+
+                                 # search_score
+                                 [:xcorr, 0.903], [:deltacn, 0.333], [:deltacnstar, "0"], [:spscore, 172.8], [:sprank, 1],
+      ])
+    end
+
+    it 'can generate correct pepxml file' do
+      
+      ## IF OUR OBJECT IS CORRECT, THEN WE GET THE OUTPUT:
+      string = @pepxml_objs.first.to_pepxml
+      ans_lines = IO.read(Tfiles + "/opd1/000.my_answer.100lines.xml").split("\n")
+      base_name_re = /base_name=".*?files\//o
+      date_re = /date=".*?"/
+      string.split("\n").each_with_index do |line,i|
+        if i > 99 ; break end
+        ans, exp = 
+          if i == 1
+            [line.sub(date_re,''), ans_lines[i].sub(date_re,'')]
+          elsif i == 2 
+            [line.sub(base_name_re,''), ans_lines[i].sub(base_name_re, '').sub(/^\s+/, "\t")]
+          elsif i == 6
+            [line.sub(base_name_re,''), ans_lines[i].sub(base_name_re, '').sub(/^\s+/, "\t\t")]
+          else
+            [line, ans_lines[i]]
+          end
+
+        #ans.split('').zip(exp.split('')) do |l,a|
+        #  if l != a
+        #    puts line
+        #    puts ans_lines[i]
+        #    puts l
+        #    puts a
+        #  end
+        #end
+        if ans != exp
+          puts ans
+          puts exp
+        end
+        ans.should == exp
+        #line.sub(base_name_re,'').should == ans_lines[i].sub(base_name_re,'')
+      end
+    end
+  end
+end
+
+
+
+describe Sequest::PepXML::Modifications do
+  before(:each) do
+    tf_params = Tfiles + "/bioworks32.params"
+    @params = Sequest::Params.new(tf_params)
+    # The params object here is completely unnecessary for this test, except
+    # that it sets up the mass table
+    @obj = Sequest::PepXML::Modifications.new(@params, "(M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000) ")
+  end
+  it 'creates a mod_symbols_hash' do
+    answ = {[:C, 12.0]=>"^", [:S, 80.0]=>"@", [:M, 29.0]=>"#", [:M, 15.9]=>"*", [:ct, 12.33]=>"[", [:nt, 14.2]=>"]"}
+    @obj.mod_symbols_hash.should == answ
+    ## need more here
+  end
+
+  it 'creates a ModificationInfo object given a special peptide sequence' do
+    mod_string = "(M* +15.90000) (M# +29.00000) (S@ +80.00000) (C^ +12.00000) (ct[ +12.33000) (nt] +14.20000) "
+    @params.diff_search_options = "15.90000 M 29.00000 M 80.00000 S 12.00000 C"
+    @params.term_diff_search_options = "14.20000 12.33000"
+    mod = Sequest::PepXML::Modifications.new(@params, mod_string)
+    ## no mods
+    peptide = "PEPTIDE"
+    mod.modification_info(peptide).should be_nil
+    peptide = "]M*EC^S@IDM#M*EMSCM["
+    modinfo = mod.modification_info(peptide)
+    modinfo.modified_peptide.should == peptide
+    modinfo.mod_nterm_mass.should be_close(146.40054, 0.000001)
+    modinfo.mod_cterm_mass.should be_close(160.52994, 0.000001)
+  end
+
+end
+
+describe Sequest::PepXML::SearchHit::ModificationInfo do
+
+  before(:each) do
+    modaaobjs = [[3, 150.3], [6, 345.2]].map do |ar| 
+      Sequest::PepXML::SearchHit::ModificationInfo::ModAminoacidMass.new(ar)
+    end
+    hash = {
+      :mod_nterm_mass => 520.2,
+      :modified_peptide => "MOD*IFI^E&D",
+      :mod_aminoacid_masses => modaaobjs,
+    }
+    #answ = "<modification_info mod_nterm_mass=\"520.2\" modified_peptide=\"MOD*IFI^E&amp;D\">\n\t<mod_aminoacid_mass position=\"3\" mass=\"150.3\"/>\n\t<mod_aminoacid_mass position=\"6\" mass=\"345.2\"/>\n</modification_info>\n"
+    @obj = Sequest::PepXML::SearchHit::ModificationInfo.new(hash)
+  end
+
+  def _re(st)
+    /#{Regexp.escape(st)}/
+  end
+  
+  it 'can produce pepxml' do
+    answ = @obj.to_pepxml
+    answ.should =~ _re('<modification_info')
+    answ.should =~ _re(" mod_nterm_mass=\"520.2\"")
+    answ.should =~ _re(" modified_peptide=\"MOD*IFI^E&amp;D\"")
+    answ.should =~ _re("<mod_aminoacid_mass")
+    answ.should =~ _re(" position=\"3\"")
+    answ.should =~ _re(" mass=\"150.3\"")
+    answ.should =~ _re(" position=\"6\"") 
+    answ.should =~ _re(" mass=\"345.2\"")
+    answ.should =~ _re("</modification_info>")
+  end
+end
+
+describe 'bioworks file with modifications transformed into pepxml' do
+
+  spec_large do
+    before(:all) do
+      modfiles_sequest_dir = Tfiles_l + '/opd1_2runs_2mods/sequest33/'
+      modfiles_data_dir = Tfiles_l + '/opd1_2runs_2mods/data/'
+      @srgfile = modfiles_sequest_dir + 'tmp.srg'
+      @out_path = modfiles_sequest_dir + 'pepxml'
+      modfiles = %w(020 040).map do |file|
+        modfiles_sequest_dir + file + ".srf"
+      end
+      objs = Sequest::PepXML.set_from_bioworks( SRFGroup.new(modfiles).to_srg(@srgfile), {:ms_data => modfiles_data_dir, :out_path => @out_path, :print => true, :backup_db_path => '/project/marcotte/marcotte/ms/database'} )
+      @out_files = %w(020 040).map do |file|
+        @out_path + '/' + file + '.xml'
+      end
+    end
+
+    after(:all) do
+      File.unlink(@srgfile) unless NODELETE
+      FileUtils.rm_r(@out_path)
+      #@out_files.each do |fn|
+      #  File.unlink(fn) unless NODELETE
+      #end
+    end
+
+    # splits string on ' 'and matches the line found by find_line_regexp in
+    # lines
+    def match_modline_pieces(lines, find_line_regexp, string)
+      pieces = string.split(' ').map {|v| /#{Regexp.escape(v)}/ }
+      lines.each do |line|
+        if line =~ find_line_regexp
+          pieces.each do |piece|
+            line.should =~ piece
+          end
+        end
+      end
+    end
+
+    it 'gets modifications right in real run' do
+      @out_files.each do |fn|
+        fn.exist_as_a_file?.should be_true
+        beginning = IO.read(fn) 
+        lines = beginning.split("\n")
+        [
+          [/aminoacid="M"/, '<aminoacid_modification symbol="*" massdiff="+15.9994" aminoacid="M" variable="Y" binary="N" mass="147.192"'],
+
+          [/aminoacid="S"/, '<aminoacid_modification symbol="#" massdiff="+79.9799" aminoacid="S" variable="Y" binary="N" mass="167.0581"'],
+          [/aminoacid="T"/, '<aminoacid_modification symbol="#" massdiff="+79.9799" aminoacid="T" variable="Y" binary="N" mass="181.085"'],
+          [/aminoacid="Y"/, '<aminoacid_modification symbol="#" massdiff="+79.9799" aminoacid="Y" variable="Y" binary="N" mass="243.1559"'],
+          [/parameter name="diff_search_options"/, '<parameter name="diff_search_options" value="15.999400 M 79.979900 STY 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>'],
+        ].each do |a,b|
+          match_modline_pieces(lines, a, b)
+        end
+        [
+        '<modification_info modified_peptide="Y#RLGGS#T#K">',
+        '<mod_aminoacid_mass position="1" mass="243.1559"/>',
+        '<mod_aminoacid_mass position="7" mass="167.0581"/>',
+        '</modification_info>',
+        '<mod_aminoacid_mass position="9" mass="181.085"/>'
+        ].each do |line|
+          beginning.should =~ /#{Regexp.escape(line)}/ # "a modification info for a peptide")
+        end
+      end
+    end
+  end
+end
+
+=end