mspire 0.4.9 → 0.5.0

data/specs/spec_id/sqt_spec.rb

@@ -1,246 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-require 'spec_id/sqt'
-require 'spec_id/srf'
-
-SpecHelperHeaderHash = {
-  'SQTGenerator' => 'mspire',
-  'SQTGeneratorVersion' => String,
-  'Database' => 'C:\\Xcalibur\\database\\ecoli_K12_ncbi_20060321.fasta',
-  'FragmentMasses' => 'AVG',
-  'PrecursorMasses' => 'AVG',
-  'StartTime' => nil, 
-  'Alg-MSModel' => 'LCQ Deca XP',
-  'Alg-PreMassUnits' => 'amu',
-  'DBLocusCount' => '4237',
-  'Alg-FragMassTol' => '1.0000',
-  'Alg-PreMassTol' => '1.4000',
-  'Alg-IonSeries' => '0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0',
-  'Alg-Enzyme' => 'Trypsin(KR/P) (2)',
-  'Comment' => ['Created from Bioworks .srf file'],
-  'StaticMod' => ['C=160.1901','Cterm=10.1230','E=161.4455'],
-  'DynamicMod' => ['STY*=+79.97990', 'M#=+14.02660'],
-}
-
-SpecHelperOtherLines =<<END
-S	2	2	1	0.0	VELA	391.04541015625	3021.5419921875	0.0	0
-S	3	3	1	0.0	VELA	446.009033203125	1743.96911621094	0.0	122
-M	1	1	445.5769264522	0.0	0.245620265603065	16.6666660308838	1	6	R.SNSK.S	U
-L	gi|16128266|ref|NP_414815.1|
-END
-
-SpecHelperOtherLinesEnd =<<END
-L	gi|90111093|ref|NP_414704.4|
-M	10	17	1298.5350544522	0.235343858599663	0.823222815990448	151.717300415039	12	54	K.LQKIITNSY*K	U
-L	gi|90111124|ref|NP_414904.2|
-END
-
-describe 'converting a large srf to sqt' do
-  def del(file)
-    if File.exist?(file)
-      File.unlink(file)
-    end
-  end
-
-  # returns true or false
-  def header_hash_match(header_lines, hash)
-    header_lines.all? do |line|
-      (h, k, v) = line.chomp.split("\t")
-      if hash[k].is_a? Array
-        if hash[k].include?(v) 
-          true
-        else
-          puts "FAILED: "
-          p k
-          p v
-          p hash[k]
-          false
-        end
-      elsif hash[k] == String
-        v.is_a?(String)
-      else
-        if v == hash[k]
-          true
-        else
-          puts "FAILED: "
-          p k
-          p v
-          p hash[k]
-          false
-        end
-      end
-    end
-  end
-
-  spec_large do
-    before(:all) do
-      @file = Tfiles_l + '/opd1_static_diff_mods/000.srf'
-      @output = Tfiles_l + '/opd1_static_diff_mods/000.sqt.tmp'
-      @srf = SRF.new(@file)
-      @original_db_filename = @srf.header.db_filename
-    end
-    it 'converts without bothering with the database' do
-      @srf.to_sqt(@output)
-      @output.exist_as_a_file?.should be_true
-      lines = File.readlines(@output)
-      lines.size.should == 80910
-      header_lines = lines.grep(/^H/)
-      (header_lines.size > 10).should be_true
-      header_hash_match(header_lines, SpecHelperHeaderHash).should be_true
-      other_lines = lines.grep(/^[^H]/)
-      other_lines[0,4].join('').should == SpecHelperOtherLines
-      other_lines[-3,3].join('').should == SpecHelperOtherLinesEnd
-      del(@output)
-    end
-    it 'warns if the db path is incorrect and we want to update db info' do
-      # requires some knowledge of how the database file is extracted
-      # internally
-      wacky_path = '/not/a/real/path/wacky.fasta'
-      @srf.header.db_filename = wacky_path
-      my_error_string = ''
-      StringIO.open(my_error_string, 'w') do |strio|
-        $stderr = strio
-        @srf.to_sqt(@output, :db_info => true)
-      end
-      my_error_string.should include(wacky_path)
-      @srf.header.db_filename = @original_db_filename
-      $stderr = STDERR
-      @output.exist_as_a_file?.should be_true
-      IO.readlines(@output).size.should == 80910
-      del(@output)
-    end
-    it 'can get db info with correct path' do
-      @srf.to_sqt(@output, :db_info => true, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest33')
-      @output.exist_as_a_file?.should be_true
-      lines = IO.readlines(@output)
-      has_md5 = lines.any? do |line|
-        line =~ /DBMD5Sum\s+202b1d95e91f2da30191174a7f13a04e/
-      end
-      has_md5.should be_true
-
-      has_seq_len = lines.any? do |line|
-        # frozen
-        line =~ /DBSeqLength\s+1342842/
-      end
-      has_seq_len.should be_true
-      lines.size.should == 80912
-      del(@output)
-    end
-    it 'can update the Database' do
-      @srf.to_sqt(@output, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest33', :update_db_path => true)
-      regexp = Regexp.new("Database\t/.*/opd1_2runs_2mods/sequest33/ecoli_K12_ncbi_20060321.fasta")
-      updated_db = IO.readlines(@output).any? do |line|
-        line =~ regexp
-      end
-      updated_db.should be_true
-      del(@output)
-    end
-  end
-end
-
-HeaderHash = {}
-header_doublets = [
-  %w(SQTGenerator	mspire),
-  %w(SQTGeneratorVersion	0.3.1),
-  %w(Database	C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta),
-  %w(FragmentMasses	AVG),
-  %w(PrecursorMasses	AVG),
-  ['StartTime', ''],
-  ['Alg-MSModel', 'LCQ Deca XP'],
-  %w(DBLocusCount	4237),
-  %w(Alg-FragMassTol	1.0000),
-  %w(Alg-PreMassTol	25.0000),
-  ['Alg-IonSeries', '0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0'],
-  %w(Alg-PreMassUnits	ppm),
-  ['Alg-Enzyme', 'Trypsin(KR/P) (2)'],
-
-  ['Comment', ['ultra small file created for testing', 'Created from Bioworks .srf file']],
-  ['DynamicMod', ['M*=+15.99940', 'STY#=+79.97990']],
-  ['StaticMod', []],
-].each do |double|
-  HeaderHash[double[0]] = double[1]
-end
-
-TestSpectra = {
-  :first => { :first_scan=>2, :last_scan=>2, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>390.92919921875, :total_intensity=>2653.90307617188, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[]},
-  :last => { :first_scan=>27, :last_scan=>27, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>393.008056640625, :total_intensity=>2896.16967773438, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[] },
-  :seventeenth => {:first_scan=>23, :last_scan=>23, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>1022.10571289062, :total_intensity=>3637.86059570312, :lowest_sp=>0.0, :num_matched_peptides=>41},
-  :first_match_17 => { :rxcorr=>1, :rsp=>5, :mh=>1022.11662242, :deltacn_orig=>0.0, :xcorr=>0.725152492523193, :sp=>73.9527359008789, :ions_matched=>6, :ions_total=>24, :sequence=>"-.MGT#TTM*GVK.L", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>0.0672458708286285, :aaseq => 'MGTTTMGVK' },
-  :last_match_17 => {:rxcorr=>10, :rsp=>16, :mh=>1022.09807242, :deltacn_orig=>0.398330867290497, :xcorr=>0.436301857233047, :sp=>49.735767364502, :ions_matched=>5, :ions_total=>21, :sequence=>"-.MRT#TSFAK.V", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>1.1, :aaseq => 'MRTTSFAK'},
-  :last_match_17_last_loci => {:reference =>'gi|16129390|ref|NP_415948.1|', :first_entry =>'gi|16129390|ref|NP_415948.1|', :locus =>'gi|16129390|ref|NP_415948.1|', :description => 'Fake description' }
-}
-
-
-describe SQT, ": reading a small sqt file" do
-  before(:each) do
-    file = Tfiles + '/small.sqt'
-    file.exist_as_a_file?.should be_true
-    @sqt = SQT.new(file)
-  end
-
-  it 'can access header entries like a hash' do
-    header = @sqt.header
-    HeaderHash.each do |k,v|
-      header[k].should == v
-    end
-  end
-
-  it 'can access header entries with methods' do
-    header = @sqt.header
-    # for example:
-    header.database.should == HeaderHash['Database']
-    # all working:
-    HeaderHash.each do |k,v|
-      header.send(SQT::Header::KeysToAtts[k]).should == v
-    end
-
-  end
-
-  it 'has spectra, matches, and loci' do
-    svt = @sqt.spectra[16]
-    reply = {:first => @sqt.spectra.first, :last => @sqt.spectra.last, :seventeenth => svt, :first_match_17 => svt.matches.first, :last_match_17 => svt.matches.last, :last_match_17_last_loci => svt.matches.last.loci.last}
-    [:first, :last, :seventeenth, :first_match_17, :last_match_17, :last_match_17_last_loci].each do |key|
-      TestSpectra[key].each do |k,v|
-        if v.is_a? Float
-          reply[key].send(k).should be_close(v, 0.0000000001)
-        else
-          reply[key].send(k).should == v
-        end
-      end
-    end
-    @sqt.spectra[16].matches.first.loci.size.should == 1
-    @sqt.spectra[16].matches.last.loci.size.should == 1
-  end
-
-end
-
-describe SQTGroup, ': acting as a SpecID on large files' do
-  spec_large do 
-    before(:each) do
-      file1 = Tfiles_l + '/opd1_2runs_2mods/sequest33/020.sqt'
-      file2 = Tfiles_l + '/opd1_2runs_2mods/sequest33/040.sqt'
-      file1.exist_as_a_file?.should be_true
-      file2.exist_as_a_file?.should be_true
-      @sqg = SQTGroup.new([file1, file2])
-    end
-
-    it 'has peptide hits' do
-      peps = @sqg.peps
-      peps.size.should == 38512  # frozen
-      # first hit in 020
-      peps.first.sequence.should == 'R.Y#RLGGS#T#K.K'
-      peps.first.base_name.should == '020'
-      # last hit in 040
-      peps.last.sequence.should == 'K.NQTNNRFK.T'
-      peps.last.base_name.should == '040'
-    end
-
-    it 'has prots' do
-      ## FROZEN:
-      @sqg.prots.size.should == 3994
-      sorted = @sqg.prots.sort_by {|v| v.reference }
-      sorted.first.reference.should == 'gi|16127996|ref|NP_414543.1|'
-      sorted.first.peps.size.should == 33
-    end
-  end
-end

data/specs/spec_id/srf_spec.rb

@@ -1,172 +0,0 @@
-
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-require File.expand_path( File.dirname(__FILE__) + '/srf_spec_helper' )
-require 'spec_id/srf'
-
-require 'fileutils'
-
-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
-
-  # given an array of out_file objects, returns the first set of hits
-  def get_first_peps(out_files)
-    out_files.each do |outf|
-      if outf.num_hits > 0
-        return outf.hits
-      end
-    end
-    return nil
-  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
-    # first available peptide hit
-    @out_files_first_pep.object_match(get_first_peps(@srf_obj.out_files).first).should be_true
-    # last available peptide hit
-    @out_files_last_pep.object_match(get_first_peps(@srf_obj.out_files.reverse).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
-
-
-Expected_hash_keys = %w(header dta_gen dta_files_first dta_files_last out_files_first out_files_last out_files_first_pep out_files_last_pep params)
-
-to_run = {
-  '3.2' => {:hash => File_32, :file => '/opd1_2runs_2mods/sequest32/020.srf'},
-  '3.3' => {:hash => File_33, :file => '/opd1_2runs_2mods/sequest33/020.srf'},
-  '3.3.1' => {:hash => File_331, :file => '/opd1_2runs_2mods/sequest331/020.srf'},
-}
-
-to_run.each do |version,info|
-  describe klass, " reading a version #{version} .srf file" do
-    spec_large do
-      before(:all) do
-        @file = Tfiles_l + info[:file]
-        Expected_hash_keys.each do |c|
-          instance_variable_set("@#{c}", info[:hash][c.to_sym])
-        end
-      end
-      it_should_behave_like "an srf reader"
-    end
-  end
-end
-
-
-describe klass, " reading a corrupted file" do
-  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 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
-
-
-# @TODO: this test needs to be created for a small mock dataset!!
-describe SRF, 'creating dta files' do
-  spec_large do 
-    before(:all) do
-      file = Tfiles_l + '/opd1_2runs_2mods/sequest33/020.srf'
-      @srf = SRF.new(file)
-    end
-
-    it 'creates dta files' do
-      @srf.to_dta_files
-      File.exist?('020').should be_true
-      File.directory?('020').should be_true
-      File.exist?('020/020.3366.3366.2.dta').should be_true
-      lines = IO.readlines('020/020.3366.3366.2.dta', "\r\n")
-      lines.first.should == "1113.106493 2\r\n"
-      lines[1].should == "164.5659 4817\r\n"
-      
-      FileUtils.rm_rf '020'
-    end
-  end
-
-end

data/specs/spec_id/srf_spec_helper.rb

@@ -1,139 +0,0 @@
-module SRFHelper
-
-  File_32 = {
-    :header => 
-    {
-      :params_filename=>"C:\\Xcalibur\\sequest\\john\\opd1_2runs_2mods\\ecoli.params",
-      :raw_filename=>"C:\\Xcalibur\\data\\john\\opd00001\\020.RAW", 
-      :modifications=>"(M* +15.99940) (STY# +79.97990)",
-      :sequest_log_filename=>"C:\\Xcalibur\\sequest\\john\\opd1_2runs_2mods\\020_sequest.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\\ecoli_K12_ncbi_20060321.fasta",
-      :enzyme=>"Enzyme:Trypsin(KR/P) (2)",
-      :version=>"3.2",
-      :model=>"LCQ Deca XP",
-      :dta_log_filename=>"C:\\Xcalibur\\sequest\\john\\opd1_2runs_2mods\\020_dta.log"
-    },
-    :dta_gen => {
-      :min_group_count => 1,
-      :start_time => 1.5,
-      :start_mass => 300.0,
-      :end_scan => 3620,
-      :group_scan => 1,
-      :start_scan => 1,
-      :num_dta_files => 3747,
-      :min_ion_threshold => 15,
-      :end_mass => 4500.0,
-    },
-    :dta_files_first => {
-
-      :mh=>390.92919921875,
-      :dta_tic=>9041311.0,
-      :num_peaks=>48,
-      :charge=>1,
-      :ms_level=>2,
-      :total_num_possible_charge_states=>0,
-    },
-    :dta_files_last => {
-      :dta_tic=>842424.0,
-      :mh=>357.041198730469,
-      :num_peaks=>78,
-      :ms_level=>2,
-      :charge=>1,
-      :total_num_possible_charge_states=>0,
-    },
-    :out_files_first => {
-      :num_hits => 0,
-      :computer => 'VELA',
-      :date_time => '05/06/2008, 02:08 PM,',
-      :hits => 0,
-    },
-    :out_files_last => {
-      :num_hits => 0,
-      :computer => 'VELA',
-      :date_time => '05/06/2008, 02:11 PM,',
-      :hits => 0,
-    },
-    :out_files_first_pep => {
-      :aaseq=>"YRLGGSTK",
-      :sequence=>"R.Y#RLGGS#T#K.K",
-      :mh=>1121.9390244522,
-      :deltacn_orig=>0.0,
-      :sp=>29.8529319763184,
-      :xcorr=>0.123464643955231,
-      :id=>2104,
-      :rsp=>1,
-      :ions_matched=>5,
-      :ions_total=>35,
-      :prots=>1,
-      :deltamass=>-0.00579976654989878,
-      :ppm=>5.16938660859491,
-      :base_name=>"020",
-      :first_scan=>3,
-      :last_scan=>3,
-      :charge=>1,
-      :deltacn=>0.795928299427032,
-      :base_name=>"020",
-    },
-    :out_files_last_pep => 
-    {
-      :aaseq=>"LLPGTARTMRR",
-      :sequence=>"R.LLPGTARTMRR.M",
-      :mh=>1272.5493424522,
-      :deltacn_orig=>0.835508584976196,
-      :deltacn=>1.1,
-      :sp=>57.9885787963867,
-      :xcorr=>0.109200321137905,
-      :id=>1361,
-      :rsp=>11,
-      :ions_matched=>6,
-      :ions_total=>40,
-      :prots=>1,
-      :deltamass=>0.00243330985608736,
-      :ppm=>1.91215729542523,
-      :base_name=>"020",
-      :first_scan=>3619,
-      :last_scan=>3619,
-      :charge=>3,
-      :deltacn=>1.1,
-      :base_name=>"020",
-    },
-
-    :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"=>"15.999400 M 79.979900 STY 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\\ecoli_K12_ncbi_20060321.fasta", "peptide_mass_tolerance"=>"25.0000", "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"=>"2", "mass_type_parent"=>"0", "match_peak_count"=>"0", "max_num_differential_per_peptide"=>"3", "ion_cutoff_percentage"=>"0.0000", "mass_type_fragment"=>"0"
-    }
-  }
-
-  File_33 = {}
-  File_32.each do |k,v|
-    File_33[k] = v.dup
-  end
-
-  ## Bioworks 3.3 (srf version 3.3)
-  File_33[:header][:raw_filename] = "C:\\Xcalibur\\data\\john\\021112-EcoliSol37-1\\020.RAW"
-  File_33[:header][:version] = "3.3"
-
-  File_33[:out_files_first][:computer] = 'TESLA'
-  File_33[:out_files_first][:date_time] = '04/24/2007, 10:41 AM,'
-  File_33[:out_files_last][:computer] = 'TESLA'
-  File_33[:out_files_last][:date_time] = '04/24/2007, 10:42 AM,'
-
-  File_33[:out_files_first_pep][:sp] = 29.8535556793213
-  File_33[:out_files_last_pep][:sp] = 57.987476348877
-  File_33[:out_files_last_pep][:rsp] = 10
-  File_33[:out_files_last_pep][:deltacn_orig] = 0.835624694824219
-
-
-  ## Bioworks 3.3.1 (srf version 3.5)
-  File_331 = {}
-  File_33.each do |k,v|
-    File_331[k] = v.dup
-  end
-  File_331[:header][:raw_filename] = "C:\\Xcalibur\\data\\john\\opd1_2runs_2mods\\020.RAW"
-  File_331[:header][:version] = "3.5"
-  File_331[:out_files_first][:date_time] = '05/06/2008, 03:31 PM,'
-  File_331[:out_files_last][:date_time] = '05/06/2008, 03:32 PM,'
-
-end
-
-

data/specs/spec_id_helper.rb

@@ -1,33 +0,0 @@
-
-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
-