mspire 0.2.4 → 0.3.0

data/test/tc_srf.rb

@@ -1,262 +0,0 @@
-
-require 'test/unit'
-require 'spec_id/srf'
-
-
-module ToMatch
-  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
-
-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 TestSRF < Test::Unit::TestCase
-  include ToMatch
-  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
-
-  def test_basic
-    if File.exist? @tfiles_l
-      ## 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)
-      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
-      assert_equal([7161, 7161, 3], @srf.index.last)
-      assert_equal([2, 2, 1], @srf.index.first)
-
-      assert_equal(@srf.index.size, @srf.dta_files.size)
-      assert_equal(@srf.out_files.size, @srf.dta_files.size)
-    else
-      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
-    end
-  end
-
-  def test_srg
-    if File.exist? @tfiles_l
-      @group.to_srg(@srg_file)
-      assert(File.exist?(@srg_file), "file exists: " + @srg_file )
-    else
-      assert_nil( puts("--SKIPPING TEST-- (missing dir: #{@tfiles_l})") )
-    end
-  end
-
-  ## treats reference special
-  def hash_match(hash, srf)
-    hash.each do |k,v|
-      if v.is_a? Float
-        delta = v/100000
-        assert_in_delta(v, srf.send(k.to_sym), delta, "param: #{k}")
-      elsif k == :reference
-        assert_equal(v[0,38], srf.prots.first.reference)
-      else
-        assert_equal(v, srf.send(k.to_sym), "param: #{k}")
-      end
-    end
-  end
-
-end
-
-