mspire 0.2.4 → 0.3.0

data/specs/spec_id/srf_spec.rb

@@ -0,0 +1,209 @@
+
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require File.expand_path( File.dirname(__FILE__) + '/srf_spec_helper' )
+require 'spec_id/srf'
+
+include SRFHelper
+
+#tfiles = File.dirname(__FILE__) + '/tfiles/'
+#tfiles_l = File.dirname(__FILE__) + '/tfiles_large/'
+#tf_srf = tfiles_l + "7MIX_STD_110802_1.srf"
+#tf_srf_inv = tfiles_l + "7MIX_STD_110802_1_INV.srf"
+#if File.exist? tfiles_l
+#  start = Time.now
+#  $group = SRFGroup.new([tf_srf, tf_srf_inv]) 
+#  $srf = $group.srfs.first
+#  puts "Time to read and compile two SRF: #{Time.now - start} secs"
+#end
+
+class Hash
+  def object_match(obj)
+    self.all? do |k,v|
+      k = k.to_sym
+      retval = 
+        if k == :peaks or k == :hits or k == :prots
+          obj.send(k).size == v
+        elsif v.class == Float
+          delta = 
+            if k == :ppm ; 0.0001          
+            else ; 0.0000001          
+            end
+          (v - obj.send(k)).abs <= delta
+        else
+          obj.send(k) == v
+        end
+      if retval == false
+        puts "BAD KEY: #{k}"
+        puts "need: #{v}"
+        puts "got: #{obj.send(k)}"
+      end
+      retval
+    end
+  end
+end
+
+klass = SRF
+
+describe 'an srf reader', :shared => true do 
+  before(:all) do
+    @srf_obj = klass.new(@file)
+  end
+
+  it 'retrieves correct header info' do
+    @header.object_match(@srf_obj.header).should be_true
+    @dta_gen.object_match(@srf_obj.header.dta_gen).should be_true
+  end
+
+  # a few more dta params could be added in here:
+  it 'retrieves correct dta files' do
+    @dta_files_first.object_match(@srf_obj.dta_files.first).should be_true
+    @dta_files_last.object_match(@srf_obj.dta_files.last).should be_true
+  end
+
+  it 'retrieves correct out files' do
+    @out_files_first.object_match(@srf_obj.out_files.first).should be_true
+    @out_files_last.object_match(@srf_obj.out_files.last).should be_true
+    @out_files_first_last_pep.object_match(@srf_obj.out_files.first.hits.last).should be_true
+    @out_files_last_last_pep.object_match(@srf_obj.out_files.last.hits.last).should be_true
+  end
+
+  xit 'retrieves correct params' do
+   @params.object_match(@srf_obj.params).should be_true
+  end
+
+  it_should 'retrieve probabilities if available'
+end
+
+
+
+describe klass, " reading a version 3.2 .srf file" do
+  spec_large do
+    before(:all) do
+      @file = Tfiles_l + '/sash7/sequest/7MIX_STD_110802_1.srf'
+      %w(header dta_gen dta_files_first dta_files_last out_files_first out_files_last out_files_first_last_pep out_files_last_last_pep params).each do |c|
+        instance_variable_set("@#{c}", File_32[c.to_sym])
+      end
+    end
+    it_should_behave_like "an srf reader"
+  end
+end
+
+
+describe klass, " reading a version 3.3 .srf file" do
+  it_should 'reading a version 3.3 .srf file'
+end
+
+
+describe klass, " reading a version 3.5 (bioworks 3.3.1) .srf file" do
+  spec_large do
+    before(:all) do
+      @file = Tfiles_l + '/sash7/sequest/bioworks331/7MIX_STD_110802_1.srf'
+      %w(header dta_gen dta_files_first dta_files_last out_files_first out_files_last out_files_first_last_pep out_files_last_last_pep params).each do |c|
+        instance_variable_set("@#{c}", File_35[c.to_sym])
+      end
+    end
+    it_should_behave_like "an srf reader"
+  end
+  it 'should read a null file from an aborted run w/o failing (but gives error msg)' do
+    file = Tfiles + '/corrupted_900.srf'
+    error_msg = Tfiles + '/error_msg.tmp'
+    File.open(error_msg, 'w') do |err_fh|
+      $stderr = err_fh
+      srf_obj = klass.new(file) 
+      srf_obj.base_name.should == '900'
+      srf_obj.params.should be_nil
+      header = srf_obj.header
+      header.db_filename.should == "C:\\Xcalibur\\database\\sf_hs_44_36f_longesttrpt.fasta.hdr"
+      header.enzyme.should == 'Enzyme:Trypsin(KR) (2)'
+      dta_gen = header.dta_gen
+      dta_gen.start_time.should be_close(1.39999997615814, 0.00000000001)
+      srf_obj.dta_files.should == []
+      srf_obj.out_files.should == []
+    end
+    IO.read(error_msg).should =~ /corrupted_900\.srf/
+    File.unlink error_msg
+  end
+
+end
+
+
+describe klass, 'reading an srf file' do
+
+  spec_large do
+    before(:all) do
+      start = Time.now
+      tf_srf = Tfiles_l + "/sash7/sequest/older/7MIX_STD_110802_1.srf"
+      @srf = klass.new(tf_srf)
+      puts "- read in #{Time.now - start} seconds"
+    end
+
+    #def initialize(arg)
+    #  super(arg)
+    #  @tfiles = File.dirname(__FILE__) + '/tfiles/'
+    #  @tfiles_l = File.dirname(__FILE__) + '/tfiles_large/'
+    #  @srg_file = @tfiles + "tmp_bioworks.srg"
+    #  @srf = $srf
+    #  @group = $group
+    #end
+
+    it 'reads' do
+    end
+
+    it 'reads an srf file (w/o probs) and extracts all basic information' do
+      ## Verify that we have everything and it is as we expect (not exhaustive)
+      head = @srf.header
+      dtgen = head.dta_gen
+      ## HEADER
+      hash_match(Header, head)
+      hash_match(Dta_gen, dtgen)
+      ## DTA_FILES
+      hash_match(Dta_files_first, @srf.dta_files.first)
+      hash_match(Dta_files_last, @srf.dta_files.last)
+      ## OUT_FILES
+      hash_match(Out_files_first, @srf.out_files.first)
+      hit = @srf.out_files.first.hits.first
+      hash_match(Out_files_first_hit, @srf.out_files.first.hits.first)
+      hash_match(Out_files_last_first_hit, @srf.out_files.last.hits.first)
+      hash_match(Out_files_last_last_hit, @srf.out_files.last.hits.last)
+      ## SEQUEST_PARAMS
+      hash_match(Sequest_params, @srf.params)
+      ## INDEX
+      @srf.index.last.should == [7161, 7161, 3]
+      @srf.index.first.should == [2, 2, 1]
+
+      @srf.dta_files.size.should == @srf.index.size
+      @srf.dta_files.size.should == @srf.out_files.size
+    end
+    it_should 'give accurate peptides' do
+    end
+  end
+
+  ## treats reference special
+  def hash_match(hash, srf)
+    hash.each do |k,v|
+      if v.is_a? Float
+        delta = v/100000
+        srf.send(k.to_sym).should be_close(v, delta)
+      elsif k == :reference
+        srf.prots.first.reference.should == v[0,38]
+      else
+        srf.send(k.to_sym).should == v
+      end
+    end
+  end
+end
+
+describe SRFGroup, 'creating an srg file' do
+
+  it 'creates one given some non-existing, relative filenames' do 
+    ## TEST SRG GROUPING:
+    filenames = %w(my/lucky/filename /another/filename)
+    @srg = SRFGroup.new
+    @srg.filenames = filenames
+    srg_file = Tfiles + '/tmp_srg_file.srg'
+    @srg.to_srg(srg_file)
+    File.exist?(srg_file).should be_true
+    File.unlink(srg_file)
+  end
+
+end

data/specs/spec_id/srf_spec_helper.rb

@@ -0,0 +1,302 @@
+module SRFHelper
+
+  File_32 = {
+    :header => 
+    {
+      :params_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\sashimi7.params",
+      :model => "LCQ Deca XP",
+      :dta_log_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\7MIX_STD_110802_1_dta.log",
+      :ion_series => "ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0",
+      :db_filename => "C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta",
+      :modifications => "",
+      :enzyme => "Enzyme:Trypsin(KR/P) (2)",
+      :sequest_log_filename => "C:\\Xcalibur\\sequest\\john\\sashimi7\\7MIX_STD_110802_1_sequest.log",
+      :version => "3.2",
+      :raw_filename => "C:\\Xcalibur\\data\\john\\sashimi7\\7MIX_STD_110802_1.RAW"
+    },
+       :dta_gen => {
+        :min_group_count => 1,
+        :start_time => 1.39999997615814,
+        :start_mass => 400.0,
+        :end_scan => 7161,
+        :group_scan => 1,
+        :start_scan => 1,
+        :num_dta_files => 6952,
+        :min_ion_threshold => 15,
+        :end_mass => 4500.0,
+      },
+      :dta_files_first => {
+        :mh => 1221.88989257812,
+        :dta_tic => 7703132.0,
+        :num_peaks => 74,
+        :charge => 1,
+        :ms_level => 2,
+        :total_num_possible_charge_states => 0,
+        :peaks => 592,
+      },
+      :dta_files_last => {
+       :mh => 2604.8360326775,
+       :dta_tic => 31977.0,
+       :num_peaks => 17,
+       :charge => 3,
+       :ms_level => 2,
+       :total_num_possible_charge_states => 0,
+       :peaks => 136,
+      },
+      :out_files_first => {
+        :num_hits => 10,
+        :computer => 'VELA',
+        :date_time => '05/12/2006, 10:58 AM,',
+        :hits => 10
+      },
+      :out_files_last => {
+         :num_hits => 10,
+         :computer => 'VELA',
+         :date_time => '05/12/2006, 11:11 AM,',
+         :hits => 10
+      },
+      :out_files_first_last_pep => {
+        :aaseq => 'QFSLSKSSLPK',
+        :sequence => 'K.QFSLSKSSLPK.S',
+        :mh => 1222.4156904522,
+        :deltacn => 1.1,
+        :sp => 57.4083709716797,
+        :xcorr => 0.802009999752045,
+        :id => 19977,
+        :rsp => 60,
+        :ions_matched => 7,
+        :ions_total => 20,
+        :prots => 1,
+        :deltamass => 0.525797874074897,
+        :ppm => 430.315265940608,
+        :base_name => '7MIX_STD_110802_1',
+        :first_scan => 2,
+        :last_scan => 2,
+        :charge => 1
+      },
+        :out_files_last_last_pep => 
+      {
+        :aaseq => 'EAFLVNSDLTLRAQLTEFRDHK',
+        :sequence => 'R.EAFLVNSDLTLRAQLTEFRDHK.L',
+        :mh => 2604.9025174522,
+        :deltacn => 1.1,
+        :sp => 26.1511478424072,
+        :xcorr => 0.634012818336487,
+        :id => 8105,
+        :rsp => 165,
+        :ions_matched => 6,
+        :ions_total => 84,
+        :prots => 1,
+        :deltamass => 0.0664847746993473,
+        :ppm => 25.523592988311,
+        :base_name => '7MIX_STD_110802_1',
+        :first_scan => 7161,
+        :last_scan => 7161,
+        :charge => 3,
+      },
+
+      :params => {
+        "add_O_Ornithine"=>"0.0000", "add_F_Phenylalanine"=>"0.0000", "add_A_Alanine"=>"0.0000", "add_C_Cysteine"=>"0.0000", "add_Y_Tyrosine"=>"0.0000", "add_X_LorI"=>"0.0000", "add_J_user_amino_acid"=>"0.0000", "add_Cterm_peptide"=>"0.0000", "add_S_Serine"=>"0.0000", "add_Nterm_protein"=>"0.0000", "add_D_Aspartic_Acid"=>"0.0000", "add_Q_Glutamine"=>"0.0000", "add_K_Lysine"=>"0.0000", "add_R_Arginine"=>"0.0000", "add_W_Tryptophan"=>"0.0000", "add_Nterm_peptide"=>"0.0000", "add_H_Histidine"=>"0.0000", "add_L_Leucine"=>"0.0000", "add_I_Isoleucine"=>"0.0000", "add_N_Asparagine"=>"0.0000", "add_B_avg_NandD"=>"0.0000", "add_Z_avg_QandE"=>"0.0000", "add_E_Glutamic_Acid"=>"0.0000", "add_G_Glycine"=>"0.0000", "add_P_Proline"=>"0.0000", "add_M_Methionine"=>"0.0000", "add_Cterm_protein"=>"0.0000", "add_V_Valine"=>"0.0000", "add_T_Threonine"=>"0.0000", "add_U_user_amino_acid"=>"0.0000", "match_peak_tolerance"=>"1.0000", "match_peak_allowed_error"=>"1", "normalize_xcorr"=>"0", "nucleotide_reading_frame"=>"0", "num_results"=>"250", "sequence_header_filter"=>"", "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y", "partial_sequence"=>"", "max_num_internal_cleavage_sites"=>"2", "search_engine"=>"SEQUEST", "print_duplicate_references"=>"40", "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", "remove_precursor_peak"=>"0", "num_output_lines"=>"10", "second_database_name"=>"", "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", "peptide_mass_tolerance"=>"1.4000", "digest_mass_range"=>"600.0 3500.0", "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P", "show_fragment_ions"=>"0", "protein_mass_filter"=>"0 0", "term_diff_search_options"=>"0.000000 0.000000", "num_description_lines"=>"5", "fragment_ion_tolerance"=>"1.0000", "peptide_mass_units"=>"0", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"1", "ion_cutoff_percentage"=>"0.0000", "mass_type_fragment"=>"0"},
+
+  }
+
+  File_35 = {}
+  File_32.each {|k,v| File_35[k] = v.dup }
+
+  File_35[:header].merge!( {
+    :sequest_log_filename => "C:\\Xcalibur\\sequest\\7MIX_STD_110802_1_sequest.log",
+    :raw_filename => "C:\\Xcalibur\\data\\john\\sash7\\7MIX_STD_110802_1.RAW", 
+    :params_filename => "C:\\Xcalibur\\sequest\\john\\bioworks331\\sashimi7.params",
+    :dta_log_filename => "C:\\Xcalibur\\sequest\\7MIX_STD_110802_1_dta.log", 
+    :version=>"3.5"
+  } )
+
+  File_35[:params].merge!( {
+  "add_O_Ornithine"=>"0.00000", "add_F_Phenylalanine"=>"0.00000", "add_A_Alanine"=>"0.00000", "add_C_Cysteine"=>"0.00000", "add_Y_Tyrosine"=>"0.00000", "add_X_LorI"=>"0.00000", "add_J_user_amino_acid"=>"0.00000", "add_Cterm_peptide"=>"0.00000", "add_S_Serine"=>"0.00000", "add_Nterm_protein"=>"0.00000", "add_D_Aspartic_Acid"=>"0.00000", "add_Q_Glutamine"=>"0.00000", "add_K_Lysine"=>"0.00000", "add_R_Arginine"=>"0.00000", "add_W_Tryptophan"=>"0.00000", "add_Nterm_peptide"=>"0.00000", "add_H_Histidine"=>"0.00000", "add_L_Leucine"=>"0.00000", "add_I_Isoleucine"=>"0.00000", "add_N_Asparagine"=>"0.00000", "add_B_avg_NandD"=>"0.00000", "add_Z_avg_QandE"=>"0.00000", "add_E_Glutamic_Acid"=>"0.00000", "add_G_Glycine"=>"0.00000", "add_P_Proline"=>"0.00000", "add_M_Methionine"=>"0.00000", "add_Cterm_protein"=>"0.00000", "add_V_Valine"=>"0.00000", "add_T_Threonine"=>"0.00000", "add_U_user_amino_acid"=>"0.00000", "match_peak_tolerance"=>"1.00000", "match_peak_allowed_error"=>"1", "normalize_xcorr"=>"0", "nucleotide_reading_frame"=>"0", "num_results"=>"250", "sequence_header_filter"=>"", "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y", "partial_sequence"=>"", "max_num_internal_cleavage_sites"=>"2", "search_engine"=>"SEQUEST", "print_duplicate_references"=>"40", "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0", "remove_precursor_peak"=>"0", "num_output_lines"=>"10", "second_database_name"=>"", "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta", "peptide_mass_tolerance"=>"1.40000", "digest_mass_range"=>"400.0000 4500.0000", "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P", "show_fragment_ions"=>"0", "protein_mass_filter"=>"0 0", "term_diff_search_options"=>"0.000000 0.000000", "num_description_lines"=>"5", "fragment_ion_tolerance"=>"1.00000", "peptide_mass_units"=>"0", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"1", "fragment_ion_units"=>"0", "ion_cutoff_percentage"=>"0.00000", "mass_type_fragment"=>"0"}
+
+  )
+
+  File_35[:out_files_first].merge!( {:computer=>'TESLA', :date_time=>'09/17/2007, 03:11 PM,'} )
+  File_35[:out_files_last].merge!( {:computer=>'TESLA', :date_time=>'09/17/2007, 03:15 PM,'} )
+  # I'm assuming this difference is due to higher precision mass...? (not a
+  # parsing error)
+  File_35[:out_files_first_last_pep][:rsp] = 56
+  File_35[:out_files_last_last_pep][:rsp] = 125
+  
+
+  Header = {
+    :db_filename => "C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta",
+    :ion_series => "ion series nABY ABCDVWXYZ: 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0",
+    :sequest_log_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\7MIX_STD_110802_1_sequest.log",
+    :raw_filename => "C:\\Xcalibur\\data\\john\\sashimi7\\7MIX_STD_110802_1.RAW",
+    :enzyme => "Enzyme:Trypsin(KR/P) (2)",
+    :params_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\sash7.params",
+    :modifications => "",
+    :version => "3.2",
+    :dta_log_filename => "C:\\Xcalibur\\sequest\\john\\db_quest\\alone_new\\sash7\\7MIX_STD_110802_1_dta.log",
+    :model => "LCQ Deca XP",
+  }
+  ## DTA Gen
+  Dta_gen = {
+    :group_scan => 1,
+    :start_time => 1.39999997615814,
+    :start_scan => 1,
+    :num_dta_files => 6952,
+    :min_ion_threshold => 15, 
+    :end_mass => 4500.0,
+    :min_group_count => 1,
+    :start_mass => 400.0,
+    :end_scan => 7161,
+  }
+  
+  Dta_files_first = {
+    :mh => 1221.88989257812,
+    :dta_tic => 7703132.0,
+    :num_peaks => 74,
+    :charge => 1,
+    :ms_level => 2,
+    :total_num_possible_charge_states => 0,
+    :peaks => "\346\214\271C\000p|F\340\016\335C\000D\fG\022l\335C\000\3604F\020\205\337C\000D~F\260\256\340C\000\020\347E\220\023\343C\000\220&F\020R\352C\000\244\313F\246\237\353C\000\360\032E\206\223\004D\000\204\030F\260\177\005D\000\346\220F \316\005D\000`\222F<\001\006D\000\356\217Fd\213\010D\000\336\tGr\314\vD\000\034}F\262\006\rD\000\026\221F\f\202!D\000\340\274E\302u#D\000\030\036Fl\275#D\000U\035G\254~&D\200\370\022H\364\315&D\000\346bGT\365&D\000\000\000@\300s5D\000`\307ET\2008D\000\3175G\310{:D\200\307\251G\230\311:D\000`5F\000\214<D\000\000\270E\254\301<D\000\340\024FX\264=D\000\270\021F\204\204?D\000\226\006H\356\256?D\000\000\000@\300\023@D\000\005\002Gb~BD\200\256\350G\032\312BD\000zAG\034\316CD\000\350\254E8\314DD\000\270\310E\316\020ED\000\010\254E\026\005QD\000\240\267E\250tSD\000tEFB\200VD\200\342\235G\374\247VD\000$\023F\000\206XD\200K\245G\242\303XD\000\343xG\270\201YD\000\214\325F\304\365ZD\0008\225FZF[D\000\230RF\232~[D@\r\201Hl\307[D\000L\031Hv\001\\D\000\3540Fx\201^D`\222\275H\f\305^D\000wZG\006\023oD\000\360\217E\354\205oD\200\335-H\350zrD\000\224,GFXtD\000\364\223F\222\201tD\200\221\341H\024\304tD\000)\034H\314\354tD\000\000\200@\022}wD\200\001\205I\274\274wD\000\t\210H\260\344wD\000\000pA\004\370yD\000@\203Eh\272\205D\2006\214Gh\336\205D\000\026\235Fb,\210D\200\177 H\\@\210D\240,\355Il`\210D\200\022\026I\320\202\210D\000 \336Fx\227\210D\000\000\200?\334{\212D\000<\252F4>\222D\000\264\213F\302\321\223D\000H\354Ed\275\230D\000-\fHv\332\230D@\313\tH\374\367\230D\000?\aG",
+  }
+  Dta_files_last = {
+    :mh => 2604.8360326775,
+    :dta_tic => 31977.0,
+    :num_peaks => 17,
+    :charge => 3,
+    :ms_level => 2,
+    :total_num_possible_charge_states => 0,
+    :peaks => "4\n\216C\000`\305D\254\205\303C\000@;D\354\321\nD\000 \275D\232\243'D\000\020iE\350\2302D\000`\245D\f\3164D\000p@E\314JID\000\300\213D\264\002PD\000\260\016E\252\213[D\0000\eE\340NoD\000@\177D0\371xD\000@:Dd\f\205D\000\000yD\200\261\215D\000@\371D\210N\221D\000`\274D\034N\256D\000\020\032EN\372\266D\000\000\aD\356\223\322D\000\250\227E"
+  }
+
+  Out_files_first = {
+    :num_hits => 10,
+    :computer => "VELA",
+    :date_time => "11/17/2006, 04:13 PM,",
+  }
+
+  Out_files_first_hit = {
+    :mh => 1220.5128044522,
+    :deltacn => 0.071944423019886, ## this is the modified version
+    :sp => 96.5815887451172,
+    :xcorr => 1.08377742767334,
+    :id => 224,
+    :rsp => 13,
+    :ions_matched => 8,
+    :ions_total => 20,
+    :sequence => "K.LCPHLTLLPGR.F",
+    :aaseq => "LCPHLTLLPGR",
+    :reference => "gi|1786425|gb|AAC73335.1| damage-inducible protein P; putative tRNA synthetase",
+    :first_scan => 2,
+    :last_scan => 2,
+    :base_name => '7MIX_STD_110802_1',
+    :charge => 1,
+  }
+
+  Out_files_last = {
+    :num_hits => 10, 
+    :computer => "VELA",
+    :date_time => "11/17/2006, 04:25 PM," ,
+  }
+  Out_files_last_first_hit = {
+    :mh => 2605.9368784522,
+    :deltacn => 0.03921128064394,
+    :sp => 76.7447052001953,
+    :xcorr => 0.915680646896362,
+    :id => 13562,
+    :rsp => 4,
+    :ions_matched => 10,
+    :ions_total => 84,
+    :sequence => "K.HLEINPNHPIVETLRQKAETHK.N",
+    :aaseq => "HLEINPNHPIVETLRQKAETHK",
+    :reference => "gi|30149327|ref|XP_293672.2| similar to ebiP7687 [Homo sapiens]",
+    :first_scan => 7161,
+    :last_scan => 7161,
+    :base_name => '7MIX_STD_110802_1',
+    :deltamass => 2605.9368784522 - 2604.8360326775,
+    :ppm => ((1.0e6 * (2605.9368784522 - 2604.8360326775)) / 2604.8360326775).abs,
+    :charge => 3,
+  }
+  Out_files_last_last_hit = {
+    :mh => 2604.9025174522,
+    :deltacn => 1.1,
+    :sp => 26.1511478424072,
+    :xcorr => 0.634012818336487,
+    :id => 8105,
+    :rsp => 165,
+    :ions_matched => 6,
+    :ions_total => 84,
+    :sequence => "R.EAFLVNSDLTLRAQLTEFRDHK.L",
+    :aaseq => "EAFLVNSDLTLRAQLTEFRDHK",
+    :reference => "gi|5453830|ref|NP_006181.1| origin recognition complex, subunit 2-like; origin",
+    :first_scan => 7161,
+    :last_scan => 7161,
+    :base_name => '7MIX_STD_110802_1',
+    :deltamass =>  2604.9025174522 - 2604.8360326775,
+    :ppm => ((1.0e6 * (2604.9025174522 - 2604.8360326775)) / 2604.8360326775).abs,
+    :charge => 3,
+  }
+  Sequest_params = {
+     "add_F_Phenylalanine"=>"0.0000",
+     "add_O_Ornithine"=>"0.0000",
+     "add_Y_Tyrosine"=>"0.0000",
+     "add_C_Cysteine"=>"0.0000",
+     "add_A_Alanine"=>"0.0000",
+     "add_J_user_amino_acid"=>"0.0000",
+     "add_X_LorI"=>"0.0000",
+     "add_S_Serine"=>"0.0000",
+     "add_Cterm_peptide"=>"0.0000",
+     "add_Q_Glutamine"=>"0.0000",
+     "add_D_Aspartic_Acid"=>"0.0000",
+     "add_Nterm_protein"=>"0.0000",
+     "add_W_Tryptophan"=>"0.0000",
+     "add_R_Arginine"=>"0.0000",
+     "add_K_Lysine"=>"0.0000",
+     "add_H_Histidine"=>"0.0000",
+     "add_Nterm_peptide"=>"0.0000",
+     "add_E_Glutamic_Acid"=>"0.0000",
+     "add_Z_avg_QandE"=>"0.0000",
+     "add_B_avg_NandD"=>"0.0000",
+     "add_N_Asparagine"=>"0.0000",
+     "add_I_Isoleucine"=>"0.0000",
+     "add_L_Leucine"=>"0.0000",
+     "add_M_Methionine"=>"0.0000",
+     "add_P_Proline"=>"0.0000",
+     "add_G_Glycine"=>"0.0000",
+     "add_U_user_amino_acid"=>"0.0000",
+     "add_T_Threonine"=>"0.0000",
+     "add_V_Valine"=>"0.0000",
+     "add_Cterm_protein"=>"0.0000",
+     "match_peak_tolerance"=>"1.0000",
+     "match_peak_allowed_error"=>"1",
+     "normalize_xcorr"=>"0",
+     "nucleotide_reading_frame"=>"0",
+     "num_results"=>"250",
+     "sequence_header_filter"=>"",
+     "diff_search_options"=>"0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y",
+     "partial_sequence"=>"",
+     "max_num_internal_cleavage_sites"=>"2",
+     "search_engine"=>"SEQUEST",
+     "print_duplicate_references"=>"40",
+     "ion_series"=>"0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0",
+     "remove_precursor_peak"=>"0",
+     "num_output_lines"=>"10",
+     "second_database_name"=>"",
+     "first_database_name"=>"C:\\Xcalibur\\database\\mixed_db_human_ecoli_7prot_unique.fasta",
+     "peptide_mass_tolerance"=>"1.4000",
+     "digest_mass_range"=>"600.0 3500.0",
+     "enzyme_info"=>"Trypsin(KR/P) 1 1 KR P",
+     "show_fragment_ions"=>"0",
+     "protein_mass_filter"=>"0 0",
+     "term_diff_search_options"=>"0.000000 0.000000",
+     "num_description_lines"=>"5",
+     "fragment_ion_tolerance"=>"1.0000",
+     "peptide_mass_units"=>"0",
+     "mass_type_parent"=>"0",
+     "match_peak_count"=>"0",
+     "max_num_differential_per_peptide"=>"1",
+     "ion_cutoff_percentage"=>"0.0000",
+     "mass_type_fragment"=>"0"
+  }
+
+end
+

data/specs/spec_id_helper.rb

@@ -0,0 +1,33 @@
+
+module SpecID::Pep
+
+  # filter must be a hash with these keys allowed:
+  # :xcorr1, :xcorr2, :xcorr3, :deltacn, :ppm, :include_deltacnstar
+  def pass_filters?(filter)
+    filter.all? do |k,v| 
+      k_as_s = k.to_s
+      if ((k_as_s[0...-1] == 'xcorr') and (k.to_s[-1,1].to_i == self.charge))
+        charge = k.to_s[-1,1].to_i
+        self.xcorr >= v
+      elsif k_as_s == 'include_deltacnstar'
+        if v == false
+          self.deltacn <= 1.0
+        else
+          true
+        end
+      elsif k_as_s == 'ppm'
+        self.send(k) <= v
+      elsif k_as_s == 'deltacn'
+        self.send(k) >= v
+      else
+        true
+      end
+    end
+  end
+
+  def fail_filters?(filter)
+    !pass_filters?(filter)
+  end
+
+end
+