mspire 0.4.9 → 0.5.0

data/specs/spec_id/protein_summary_spec.rb

@@ -1,189 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-require 'spec_id/protein_summary'
-
-xdescribe ProteinSummary do
-
-  before(:all) do
-    @tf_proph = Tfiles_l + "/opd1/000_020-prot.xml"
-    @tf_summary = Tfiles_l + "/opd1/000_020-prot.summary.html"
-    @tf_bioworks_small = Tfiles + '/bioworks_small.xml'
-    @tf_bioworks_small_summary_html = Tfiles + '/bioworks_small.summary.html'
-    @tf_proph_cat_inv =  Tfiles + '/opd1/opd1_cat_inv_small-prot.xml'
-    @tf_proph_cat_inv_summary_html = Tfiles + '/opd1/opd1_cat_inv_small-prot.summary.html'
-    @tf_proph_cat_inv_summary_png = Tfiles + '/opd1/opd1_cat_inv_small-prot.summary.png'
-    @tf_peptide_count = Tfiles + "/peptide_counts.tmp.txt"
-    @no_delete = false
-  end
-
-  spec_large do
-    it 'does basic summary on prophet file' do
-      runit "-c 5.0 #{@tf_proph}"
-      @tf_summary.exist_as_a_file?.should be_true
-      string = IO.read(@tf_summary)
-      string.should =~ /gi\|16132176\|ref\|NP_418775\.1\|/
-      string.should =~ /16132176/
-      File.unlink(@tf_summary) unless @no_delete
-    end
-  end
-
-  it 'does basic summary on bioworks.xml file' do
-    runit "#{@tf_bioworks_small}"
-    @tf_bioworks_small_summary_html.exist_as_a_file?.should be_true
-    File.unlink @tf_bioworks_small_summary_html unless @no_delete
-    # @TODO: need to freeze the output here
-  end
-
-
-  it 'calculates precision values with bioworks files' do
-    ## Could reimplement a separate file approach?
-    #reply = `#{@cmd} -f #{@tf_bioworks_small} #{@tf_bioworks_small} --precision`
-    runit "#{@tf_bioworks_small} --precision"
-    IO.read(@tf_bioworks_small_summary_html).should =~ /# hits.*106/m
-    # should add more tests here...
-    @tf_bioworks_small_summary_html.exist_as_a_file?.should be_true
-    File.unlink @tf_bioworks_small_summary_html unless @no_delete
-  end
-
-  it 'calculates precision values with prophet files' do
-    runit "#{@tf_proph_cat_inv} -f INV_ --prefix --precision"
-    html =  IO.read(@tf_proph_cat_inv_summary_html)
-    html.should =~ /# hits/
-    html.should =~ /2.*0\.0000/m
-    html.should =~ /3.*0\.3333/m
-    html.should =~ /7.*0\.5714/m
-
-    File.unlink @tf_proph_cat_inv_summary_html unless @no_delete
-    File.unlink @tf_proph_cat_inv_summary_png unless @no_delete
-  end
-
-  spec_large do
-    it 'gives correct peptide counts' do
-      runit "-c 5.0 #{@tf_proph} --peptide_count #{@tf_peptide_count}"
-      @tf_peptide_count.exist_as_a_file?.should be_true
-      file = IO.read(@tf_peptide_count)
-      file.should include("gi|16132176|ref|NP_418775.1|\t2")
-      file.should include("gi|16131996|ref|NP_418595.1|\t1")
-      file.should include("gi|16131692|ref|NP_418288.1|\t4")
-      File.unlink @tf_peptide_count unless @no_delete
-    end
-  end
-
-  def runit(string_or_args)
-    args = if string_or_args.is_a? String
-             string_or_args.split(/\s+/)
-           else
-             string_or_args
-           end
-    ProteinSummary.new.create_from_command_line_args(args) 
-  end
-
-
-  end
-
-
-=begin
-
-require 'test/unit'
-require 'spec_id/protein_summary'
-require File.dirname(__FILE__) + '/test_helper'
-
-
-
-class ProphProtSummaryTest < Test::Unit::TestCase
-
-  NODELETE = false
-
-  def initialize(arg)
-    super(arg)
-    @tfiles = File.dirname(__FILE__) + '/tfiles/'
-    @tfiles_l = File.dirname(__FILE__) + '/tfiles_large/'
-    @tf_proph = @tfiles_l + "opd1/000_020-prot.xml"
-    @tf_summary = @tfiles_l + "opd1/000_020-prot.summary.html"
-    @tf_bioworks_small = @tfiles + 'bioworks_small.xml'
-    @tf_bioworks_small_summary_html = @tfiles + 'bioworks_small.summary.html'
-    @tf_proph_cat_inv =  @tfiles + 'opd1/opd1_cat_inv_small-prot.xml'
-    @tf_proph_cat_inv_summary_html = @tfiles + 'opd1/opd1_cat_inv_small-prot.summary.html'
-    @tf_proph_cat_inv_summary_png = @tfiles + 'opd1/opd1_cat_inv_small-prot.summary.png'
-    @tf_peptide_count = @tfiles + "peptide_counts.tmp.txt"
-  end
-
-  def runit(string_or_args)
-    args = if string_or_args.is_a? String
-             string_or_args.split(/\s+/)
-           else
-             string_or_args
-           end
-    ProteinSummary.new.create_from_command_line_args(args) 
-  end
-
- 
-  def test_usage
-    output = capture_stdout {
-      runit('')
-    }
-    assert_match(/usage:/, output)
-  end
-
-  def test_proph_basic
-    if File.exist? @tfiles_l
-      runit "-c 5.0 #{@tf_proph}"
-      ProteinSummary.new.create_from_command_line_args([@tf_proph, '-c', '5.0'])
-      assert(File.exist?(@tf_summary), "file #{@tf_summary} exists")
-      string = IO.read(@tf_summary)
-      assert_match(/gi\|16132176\|ref\|NP_418775\.1\|/, string)
-      assert_match(/16132176/, string)
-      File.unlink(@tf_summary) unless NODELETE
-    else
-      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
-    end
-  end
-
-  def test_bioworks_basic
-    runit "#{@tf_bioworks_small}"
-    assert(File.exist?(@tf_bioworks_small_summary_html), "file #{@tf_bioworks_small_summary_html} exists")
-    File.unlink @tf_bioworks_small_summary_html unless NODELETE
-
-    # @TODO: need to freeze the output here
-  end
-
-  def test_bioworks_with_precision
-    ## Could reimplement a separate file approach?
-    #reply = `#{@cmd} -f #{@tf_bioworks_small} #{@tf_bioworks_small} --precision`
-    runit "#{@tf_bioworks_small} --precision"
-    assert_match(/# hits.*106/m, IO.read(@tf_bioworks_small_summary_html))
-    #assert_match(/False Positive Rate.*: 0.500/, IO.read(@tf_bioworks_small_summary_html))
-    #assert_match(/False Positive Rate.*: 0.500/, IO.read(@tf_bioworks_small_summary_html))
-    assert(File.exist?(@tf_bioworks_small_summary_html), "file #{@tf_bioworks_small_summary_html} exists")
-    File.unlink @tf_bioworks_small_summary_html unless NODELETE
-  end
-
-  def test_proph_with_precision
-    #puts @cmd
-    runit "#{@tf_proph_cat_inv} -f INV_ --prefix --precision"
-    html =  IO.read(@tf_proph_cat_inv_summary_html)
-    assert_match(/# hits/, html, "in #{@tf_proph_cat_inv_summary_html}")
-    assert_match(/2.*0\.0000/m, html, "in #{@tf_proph_cat_inv_summary_html}")
-    assert_match(/3.*0\.3333/m, html, "in #{@tf_proph_cat_inv_summary_html}")
-    assert_match(/7.*0\.5714/m, html, "in #{@tf_proph_cat_inv_summary_html}")
-
-    File.unlink @tf_proph_cat_inv_summary_html unless NODELETE
-    File.unlink @tf_proph_cat_inv_summary_png unless NODELETE
-  end
-
-  def test_peptide_count
-    if File.exist? @tfiles_l
-      runit "-c 5.0 #{@tf_proph} --peptide_count #{@tf_peptide_count}"
-      assert(File.exist?(@tf_peptide_count), "file #{@tf_peptide_count} exists")
-      file = IO.read(@tf_peptide_count)
-      assert_match("gi|16132176|ref|NP_418775.1|\t2", file)
-      assert_match("gi|16131996|ref|NP_418595.1|\t1", file)
-      assert_match("gi|16131692|ref|NP_418288.1|\t4", file)
-      File.unlink @tf_peptide_count unless NODELETE
-    else
-      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
-    end
-  end
-
-end
-
-=end

data/specs/spec_id/sequest/params_spec.rb

@@ -1,68 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
-require 'spec_id/sequest/params'
-
-
-describe "a sequest params object", :shared => true do
-  before(:each) do
-    @obj = Sequest::Params.new(@file)
-  end
-  it 'gives enzyme_specificity' do
-    ar = @obj.enzyme_specificity
-    ar.size.should == 3
-    ar.should == @enzyme_specificity
-  end
-  it 'returns static mods callable by key' do
-    @obj.add_Cterm_peptide.should == @add_Cterm_peptide
-  end
-end
-
-
-describe Sequest::Params, "with a bioworks 3.1 params" do
-  before(:all) do
-    @file = Tfiles + '/bioworks31.params'
-    @obj = Sequest::Params.new(@file)
-    @enzyme_specificity = [1, 'KR', '']
-    @add_Cterm_peptide = '0.0000'
-  end
-  it_should_behave_like 'a sequest params object'
-end
-
-describe Sequest::Params, "with a bioworks 3.2 params" do
-  before(:all) do
-    @file = Tfiles + '/bioworks32.params'
-    @obj = Sequest::Params.new(@file)
-    @enzyme_specificity = [1, 'KR', 'P']
-    @add_Cterm_peptide = '0.0000'
-  end
-  it_should_behave_like 'a sequest params object'
-end
-
-describe Sequest::Params, "with a bioworks 3.3 params" do
-  before(:all) do
-    @file = Tfiles + '/bioworks33.params'
-    @obj = Sequest::Params.new(@file)
-    @enzyme_specificity = [1, 'KR', '']
-    @add_Cterm_peptide = '0.0000'
-  end
-  it_should_behave_like 'a sequest params object'
-end
-
-describe Sequest::Params, "given a bioworks 3.2 params (from .srf file)" do
-  before(:all) do
-    @file = Tfiles + '/7MIX_STD_110802_1.sequest_params_fragment.srf'
-    @obj = Sequest::Params.new(@file)
-    @enzyme_specificity = [1, 'KR', 'P']
-    @add_Cterm_peptide = '0.0000'
-  end
-  it_should_behave_like 'a sequest params object'
-end
-
-
-describe Sequest::Params do
-  it '(private) can give a system independent basename' do
-    Sequest::Params.new._sys_ind_basename("C:\\Xcalibur\\database\\hello.fasta").should == "hello.fasta"
-    Sequest::Params.new._sys_ind_basename("/work/john/hello.fasta").should == "hello.fasta"
-  end
-  
-end
-

data/specs/spec_id/sequest/pepxml_spec.rb

@@ -1,374 +0,0 @@
-
-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
-

data/specs/spec_id/sequest_spec.rb

@@ -1,38 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-require 'spec_id'
-require 'spec_id/sequest'
-require 'set'
-
-class MockPepHit
-  attr_accessor :first_scan, :xcorr, :idd
-  def initialize(*args)
-    (@first_scan, @xcorr, @idd) = args
-  end
-end
-
-describe Sequest, ": with small mock set" do
-  before(:each) do
-    index = 0
-    hits = [[0, 5.0, 0], [0, 4.0, 1], [0, 3.0, 2], 
-      [1, 5.0, 3], [1, 4.0, 4],
-      [2, 5.5, 5], 
-      [3, 5.5, 6], [3, 5.5, 7], [3, 4.0, 8], [3, 2.4, 9], [3, 2.4, 10]
-    ].map do |hit|
-      MockPepHit.new(*hit)
-    end
-    @peps = hits.sort_by {rand}
-  end
-
-  it 'returns "other" hits' do
-    included = [2, 8, 9, 10]
-    first_index = 2
-    last_index = 10
-    reply = Sequest.other_hits(@peps, first_index,last_index,:first_scan, [:xcorr, {:down => :xcorr}])
-    reply.map {|hit| hit.idd }.to_set.should == included.to_set
-
-    # same, but optimized
-    reply = Sequest.other_hits_sorted_by_xcorr(@peps, first_index,last_index,:first_scan)
-    reply.map {|hit| hit.idd }.to_set.should == included.to_set
-  end
-
-end