ms-sequest 0.0.11 → 0.0.12

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Files changed (36) hide show
  1. data/.autotest +14 -0
  2. data/.gitignore +8 -0
  3. data/.gitmodules +9 -0
  4. data/History +8 -0
  5. data/{MIT-LICENSE → LICENSE} +1 -0
  6. data/README.rdoc +77 -0
  7. data/Rakefile +110 -0
  8. data/VERSION +1 -0
  9. data/lib/ms/sequest.rb +1 -1
  10. data/lib/ms/sequest/bioworks.rb +498 -0
  11. data/lib/ms/sequest/pepxml.rb +1458 -0
  12. data/lib/ms/sequest/srf.rb +4 -3
  13. data/lib/ms/sequest/srf/search.rb +1 -1
  14. data/lib/ms/sequest/srf/search/tap.rb +1 -1
  15. data/script/fasta_ipi_to_ncbi-ish.rb +29 -0
  16. data/spec/ms/sequest/bioworks_spec.rb +153 -0
  17. data/spec/ms/sequest/params_spec.rb +131 -0
  18. data/spec/ms/sequest/pepxml_spec.rb +376 -0
  19. data/spec/ms/sequest/sqt_spec.rb +78 -0
  20. data/spec/ms/sequest/sqt_spec_helper.rb +34 -0
  21. data/spec/ms/sequest/srf/search_spec.rb +53 -0
  22. data/spec/ms/sequest/srf/search_spec_helper.rb +341 -0
  23. data/spec/ms/sequest/srf/sqt_spec.rb +142 -0
  24. data/spec/ms/sequest/srf_spec.rb +182 -0
  25. data/spec/ms/sequest/srf_spec_helper.rb +172 -0
  26. data/spec/spec_helper.rb +51 -0
  27. data/spec/testfiles/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  28. data/spec/testfiles/bioworks31.params +77 -0
  29. data/spec/testfiles/bioworks32.params +62 -0
  30. data/spec/testfiles/bioworks33.params +63 -0
  31. data/spec/testfiles/corrupted_900.srf +0 -0
  32. data/spec/testfiles/small.sqt +87 -0
  33. data/spec/testfiles/small2.sqt +176 -0
  34. data/tap.yml +0 -0
  35. metadata +74 -21
  36. data/README +0 -23
data/spec/spec_helper.rb ADDED
@@ -0,0 +1,51 @@
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+
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+ require 'rubygems'
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+ require 'spec/more'
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+
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+ # This is already defined in our module
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+ #TESTFILES = File.expand_path(File.dirname(__FILE__)) + '/testfiles'
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+
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+ Bacon.summary_on_exit
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+
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+ #module Bacon
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+ # class Context
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+ # def hash_match(hash, obj)
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+ # hash.each do |k,v|
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+ # if v.is_a?(Hash)
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+ # hash_match(v, obj.send(k.to_sym))
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+ # else
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+ # puts "#{k}: #{v} but was #{obj.send(k.to_sym)}" if obj.send(k.to_sym) != v
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+ # obj.send(k.to_sym).should.equal v
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+ # end
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+ # end
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+ # end
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+ # end
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+ #end
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+
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+
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+ TESTFILES = File.expand_path(File.dirname(__FILE__)) + "/testfiles"
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+
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+ begin
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+ require 'ms/testdata'
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+ rescue(LoadError)
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+ puts %Q{
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+ Tests probably cannot be run because the submodules have
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+ not been initialized. Use these commands and try again:
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+
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+ % git submodule init
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+ % git submodule update
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+
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+ }
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+ raise
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+ end
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+
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+ def capture_stderr
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+ begin
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+ $stderr = StringIO.new
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+ yield
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+ $stderr.rewind && $stderr.read
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+ ensure
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+ $stderr = STDERR
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+ end
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+ end
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+
data/spec/testfiles/bioworks31.params ADDED
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+ [SEQUEST]
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+ first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
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+ second_database_name =
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+ peptide_mass_tolerance = 1.5000
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+ ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
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+ fragment_ion_tolerance = 0.0000 ; leave at 0.0 unless you have real poor data
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+ num_output_lines = 10 ; # peptide results to show
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+ num_results = 500 ; # results to store
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+ num_description_lines = 5 ; # full protein descriptions to show for top N peptides
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+ show_fragment_ions = 1 ; 0=no, 1=yes
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+ print_duplicate_references = 40 ; 0=no, 1=yes
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+ enzyme_number = 1
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+ max_num_differential_AA_per_mod = 4 ; max # of modified AA per diff. mod in a peptide
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+ diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
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+ term_diff_search_options = 0.0000 0.0000
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+ nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
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+ mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
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+ mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
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+ normalize_xcorr = 0 ; use normalized xcorr values in the out file
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+ remove_precursor_peak = 0 ; 0=no, 1=yes
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+ ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
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+ max_num_internal_cleavage_sites = 2 ; maximum value is 5
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+ protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
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+ match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
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+ match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
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+ match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
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+ create_output_files = 1 ; 0=no, 1=yes
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+ partial_sequence =
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+ sequence_header_filter =
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+
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+ add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
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+ add_Cterm_protein = 0.0000 ; added to each protein C-terminus
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+ add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
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+ add_Nterm_protein = 0.0000 ; added to each protein N-terminus
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+ add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146
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+ add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711
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+ add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303
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+ add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276
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+ add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841
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+ add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768
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+ add_C_Cysteine = 0.0000 ; added to C - avg. 103.1388, mono. 103.00919
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+ add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406
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+ add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406
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+ add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
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+ add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
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+ add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
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+ add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
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+ add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
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+ add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
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+ add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
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+ add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
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+ add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
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+ add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
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+ add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
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+ add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
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+ add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
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+ add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
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+ add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931
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+
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+ [SEQUEST_ENZYME_INFO]
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+ 0. No_Enzyme 0 - -
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+ 1. Trypsin 1 KR -
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+ 2. Trypsin(KRLNH) 1 KRLNH -
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+ 3. Chymotrypsin 1 FWYL -
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+ 4. Chymotrypsin(FWY) 1 FWY P
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+ 5. Clostripain 1 R -
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+ 6. Cyanogen_Bromide 1 M -
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+ 7. IodosoBenzoate 1 W -
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+ 8. Proline_Endopept 1 P -
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+ 9. Staph_Protease 1 E -
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+ 10. Trypsin_K 1 K P
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+ 11. Trypsin_R 1 R P
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+ 12. GluC 1 ED -
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+ 13. LysC 1 K -
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+ 14. AspN 0 D -
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+ 15. Elastase 1 ALIV P
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+ 16. Elastase/Tryp/Chymo 1 ALIVKRWFY P
data/spec/testfiles/bioworks32.params ADDED
@@ -0,0 +1,62 @@
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+ [SEQUEST]
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+ first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
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+ second_database_name =
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+ peptide_mass_tolerance = 1.4000
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+ peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
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+ ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
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+ fragment_ion_tolerance = 1.0000 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
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+ num_output_lines = 10 ; # peptide results to show
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+ num_results = 250 ; # results to store
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+ num_description_lines = 5 ; # full protein descriptions to show for top N peptides
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+ show_fragment_ions = 0 ; 0=no, 1=yes
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+ print_duplicate_references = 40 ; number of duplicate references reported
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+ enzyme_info = Trypsin(KR/P) 1 1 KR P
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+ max_num_differential_per_peptide = 1 ; max # of diff. mod in a peptide
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+ diff_search_options = 0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
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+ term_diff_search_options = 0.000000 0.000000
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+ nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
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+ mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
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+ mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
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+ normalize_xcorr = 0 ; use normalized xcorr values in the out file
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+ remove_precursor_peak = 0 ; 0=no, 1=yes
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+ ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
23
+ max_num_internal_cleavage_sites = 2 ; maximum value is 12
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+ protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
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+ match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
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+ match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
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+ match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
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+ partial_sequence =
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+ sequence_header_filter =
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+ digest_mass_range = 600.0 3500.0
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+
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+ add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
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+ add_Cterm_protein = 0.0000 ; added to each protein C-terminus
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+ add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
35
+ add_Nterm_protein = 0.0000 ; added to each protein N-terminus
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+ add_G_Glycine = 0.0000 ; added to G
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+ add_A_Alanine = 0.0000 ; added to A
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+ add_S_Serine = 0.0000 ; added to S
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+ add_P_Proline = 0.0000 ; added to P
40
+ add_V_Valine = 0.0000 ; added to V
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+ add_T_Threonine = 0.0000 ; added to T
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+ add_C_Cysteine = 0.0000 ; added to C
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+ add_L_Leucine = 0.0000 ; added to L
44
+ add_I_Isoleucine = 0.0000 ; added to I
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+ add_X_LorI = 0.0000 ; added to X
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+ add_N_Asparagine = 0.0000 ; added to N
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+ add_O_Ornithine = 0.0000 ; added to O
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+ add_B_avg_NandD = 0.0000 ; added to B
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+ add_D_Aspartic_Acid = 0.0000 ; added to D
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+ add_Q_Glutamine = 0.0000 ; added to Q
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+ add_K_Lysine = 0.0000 ; added to K
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+ add_Z_avg_QandE = 0.0000 ; added to Z
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+ add_E_Glutamic_Acid = 0.0000 ; added to E
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+ add_M_Methionine = 0.0000 ; added to M
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+ add_H_Histidine = 0.0000 ; added to H
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+ add_F_Phenylalanine = 0.0000 ; added to F
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+ add_R_Arginine = 0.0000 ; added to R
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+ add_Y_Tyrosine = 0.0000 ; added to Y
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+ add_W_Tryptophan = 0.0000 ; added to W
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+ add_J_user_amino_acid = 0.0000 ; added to J
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+ add_U_user_amino_acid = 0.0000 ; added to U
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+
data/spec/testfiles/bioworks33.params ADDED
@@ -0,0 +1,63 @@
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+ [SEQUEST]
2
+ first_database_name = C:\Xcalibur\database\yeast.fasta
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+ second_database_name =
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+ peptide_mass_tolerance = 2.0000
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+ peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
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+ ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
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+ fragment_ion_tolerance = 1.0000 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
8
+ fragment_ion_units = 0 ; 0=amu, 1=mmu
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+ num_output_lines = 10 ; # peptide results to show
10
+ num_results = 250 ; # results to store
11
+ num_description_lines = 5 ; # full protein descriptions to show for top N peptides
12
+ show_fragment_ions = 0 ; 0=no, 1=yes
13
+ print_duplicate_references = 0 ; number of duplicate references reported
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+ enzyme_info = Trypsin(KR) 1 1 KR -
15
+ max_num_differential_per_peptide = 3 ; max # of diff. mod in a peptide
16
+ diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
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+ term_diff_search_options = 0.0000 0.0000
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+ nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
19
+ mass_type_parent = 1 ; 0=average masses, 1=monoisotopic masses
20
+ mass_type_fragment = 1 ; 0=average masses, 1=monoisotopic masses
21
+ normalize_xcorr = 0 ; use normalized xcorr values in the out file
22
+ remove_precursor_peak = 0 ; 0=no, 1=yes
23
+ ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
24
+ max_num_internal_cleavage_sites = 2 ; maximum value is 12
25
+ protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
26
+ match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
27
+ match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
28
+ match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
29
+ partial_sequence =
30
+ sequence_header_filter =
31
+ digest_mass_range = 600.0000 4500.0000
32
+
33
+ add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
34
+ add_Cterm_protein = 0.0000 ; added to each protein C-terminus
35
+ add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
36
+ add_Nterm_protein = 0.0000 ; added to each protein N-terminus
37
+ add_G_Glycine = 0.0000 ; added to G
38
+ add_A_Alanine = 0.0000 ; added to A
39
+ add_S_Serine = 0.0000 ; added to S
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+ add_P_Proline = 0.0000 ; added to P
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+ add_V_Valine = 0.0000 ; added to V
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+ add_T_Threonine = 0.0000 ; added to T
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+ add_C_Cysteine = 0.0000 ; added to C
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+ add_L_Leucine = 0.0000 ; added to L
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+ add_I_Isoleucine = 0.0000 ; added to I
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+ add_X_LorI = 0.0000 ; added to X
47
+ add_N_Asparagine = 0.0000 ; added to N
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+ add_O_Ornithine = 0.0000 ; added to O
49
+ add_B_avg_NandD = 0.0000 ; added to B
50
+ add_D_Aspartic_Acid = 0.0000 ; added to D
51
+ add_Q_Glutamine = 0.0000 ; added to Q
52
+ add_K_Lysine = 0.0000 ; added to K
53
+ add_Z_avg_QandE = 0.0000 ; added to Z
54
+ add_E_Glutamic_Acid = 0.0000 ; added to E
55
+ add_M_Methionine = 0.0000 ; added to M
56
+ add_H_Histidine = 0.0000 ; added to H
57
+ add_F_Phenylalanine = 0.0000 ; added to F
58
+ add_R_Arginine = 0.0000 ; added to R
59
+ add_Y_Tyrosine = 0.0000 ; added to Y
60
+ add_W_Tryptophan = 0.0000 ; added to W
61
+ add_J_user_amino_acid = 0.0000 ; added to J
62
+ add_U_user_amino_acid = 0.0000 ; added to U
63
+
data/spec/testfiles/small.sqt ADDED
@@ -0,0 +1,87 @@
1
+ H SQTGenerator mspire
2
+ H SQTGeneratorVersion 0.3.1
3
+ H Database C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
4
+ H FragmentMasses AVG
5
+ H PrecursorMasses AVG
6
+ H StartTime
7
+ H Alg-MSModel LCQ Deca XP
8
+ H DBLocusCount 4237
9
+ H Alg-FragMassTol 1.0000
10
+ H Alg-PreMassTol 25.0000
11
+ H Alg-IonSeries 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
12
+ H Alg-PreMassUnits ppm
13
+ H Alg-Enzyme Trypsin(KR/P) (2)
14
+ H Comment ultra small file created for testing
15
+ H Comment Created from Bioworks .srf file
16
+ H DynamicMod M*=+15.99940
17
+ H DynamicMod STY#=+79.97990
18
+ S 2 2 1 0.0 TESLA 390.92919921875 2653.90307617188 0.0 0
19
+ S 3 3 1 0.0 TESLA 1121.94482421875 3283.54272460938 0.0 3
20
+ M 1 1 1121.93902442 0.0 0.123464643955231 29.8535556793213 5 35 R.Y#RLGGS#T#K.K U
21
+ L gi|16130113|ref|NP_416680.1|
22
+ M 2 2 1121.96119642 0.795928299427032 0.0251956433057785 11.7253675460815 6 28 K.S#GNDLHY#R.G U
23
+ L gi|16128318|ref|NP_414867.1|
24
+ S 4 4 1 0.0 TESLA 1321.91357421875 3445.47338867188 0.0 0
25
+ S 6 6 1 0.0 TESLA 391.016235351562 2796.34912109375 0.0 0
26
+ S 7 7 1 0.0 TESLA 1221.97802734375 3769.00024414062 0.0 0
27
+ S 8 8 1 0.0 TESLA 1322.00439453125 3935.37475585938 0.0 0
28
+ S 10 10 1 0.0 TESLA 1121.91625976562 3106.53686523438 0.0 18
29
+ M 1 5 1121.91159842 0.0 0.517962515354156 33.0886917114258 6 24 K.Y#DTEDY#R.H U
30
+ L gi|16128388|ref|NP_414937.1|
31
+ M 2 9 1121.91159842 0.17718294262886 0.426188379526138 28.0216407775879 6 24 K.Y#DT#EDYR.H U
32
+ L gi|16128388|ref|NP_414937.1|
33
+ M 3 3 1121.89096442 0.488175302743912 0.265105992555618 39.1714057922363 8 35 R.TTEKS#S#T#K.S U
34
+ L gi|16130334|ref|NP_416903.1|
35
+ M 4 2 1121.93902442 0.631783962249756 0.190722107887268 41.4820594787598 7 35 R.Y#RLGGS#T#K.K U
36
+ L gi|16130113|ref|NP_416680.1|
37
+ M 5 1 1121.89757842 0.707324922084808 0.15159472823143 41.5733528137207 8 30 R.FT#T#HGY#R.D U
38
+ L gi|16129410|ref|NP_415968.1|
39
+ M 6 13 1121.91159842 0.767382383346558 0.120487198233604 11.1207275390625 5 24 K.YDT#EDY#R.H U
40
+ L gi|16128388|ref|NP_414937.1|
41
+ M 7 14 1121.91785042 0.896376550197601 0.0536730699241161 6.10089921951294 4 25 R.NCY#Y#Y#R.E U
42
+ L gi|16128767|ref|NP_415320.1|
43
+ M 8 6 1121.89096442 0.931291460990906 0.0355884432792664 32.6543502807617 6 35 R.T#T#EKS#STK.S U
44
+ L gi|16130334|ref|NP_416903.1|
45
+ S 11 11 1 0.0 TESLA 1222.03955078125 3505.90185546875 0.0 6
46
+ M 1 1 1222.02947242 0.0 0.258438050746918 134.970413208008 10 36 R.EDDS#PQGS#VK.A U
47
+ L gi|16129012|ref|NP_415567.1|
48
+ M 2 2 1222.04971442 0.24978731572628 0.193883508443832 59.2804641723633 8 32 R.S#YDT#EDGM*K.F U
49
+ L gi|90111504|ref|NP_417349.4|
50
+ M 3 2 1222.04971442 0.362763434648514 0.164686173200607 59.2804641723633 8 32 R.SY#DT#EDGM*K.F U
51
+ L gi|90111504|ref|NP_417349.4|
52
+ M 4 3 1222.05213042 0.740513622760773 0.067061148583889 45.5321998596191 7 35 K.QIT#T#Y#LDK.G U
53
+ L gi|49176305|ref|YP_026198.1|
54
+ S 14 14 1 0.0 TESLA 371.043518066406 3490.9755859375 0.0 0
55
+ S 15 15 2 0.0 TESLA 814.180101299688 5307.74365234375 0.0 0
56
+ S 15 15 3 0.0 TESLA 1220.76651363453 5307.74365234375 0.0 0
57
+ S 16 16 1 0.0 TESLA 362.151611328125 4569.6455078125 0.0 0
58
+ S 18 18 2 0.0 TESLA 616.584642315313 3327.263671875 0.0 4
59
+ M 1 3 616.58129342 0.0 0.0607584044337273 8.33333301544189 1 12 K.S#KSSK.E U
60
+ L gi|16129674|ref|NP_416233.1|
61
+ S 18 18 3 0.0 TESLA 924.373325157969 3327.263671875 0.0 0
62
+ S 19 19 1 0.0 TESLA 444.983337402344 1700.27795410156 0.0 0
63
+ S 20 20 1 0.0 TESLA 361.671875 4756.20703125 0.0 0
64
+ S 23 23 1 0.0 TESLA 1022.10571289062 3637.86059570312 0.0 41
65
+ M 1 5 1022.11662242 0.0 0.725152492523193 73.9527359008789 6 24 -.MGT#TTM*GVK.L U
66
+ L gi|16128980|ref|NP_415534.1|
67
+ M 2 5 1022.11662242 0.0672458708286285 0.67638897895813 73.9527359008789 6 24 -.MGTT#TM*GVK.L U
68
+ L gi|16128980|ref|NP_415534.1|
69
+ M 3 3 1022.09997242 0.162994727492332 0.606956422328949 90.1473388671875 6 14 K.NQTNNRFK.T U
70
+ L gi|16131314|ref|NP_417899.1|
71
+ M 4 1 1022.11662242 0.169317632913589 0.602371394634247 127.829414367676 8 21 -.MT#M*NITSK.Q U
72
+ L gi|16130518|ref|NP_417088.1|
73
+ M 5 10 1022.11662242 0.205745562911034 0.57595556974411 60.3448905944824 5 24 -.MGTTT#M*GVK.L U
74
+ L gi|16128980|ref|NP_415534.1|
75
+ M 6 11 1022.11662242 0.264144241809845 0.533607602119446 60.1143188476562 5 21 -.MTM*NITS#K.Q U
76
+ L gi|16130518|ref|NP_417088.1|
77
+ M 7 8 1022.11662242 0.331606924533844 0.484686881303787 67.8056793212891 5 21 -.MTM*NIT#SK.Q U
78
+ L gi|16130518|ref|NP_417088.1|
79
+ M 8 16 1022.09807242 0.380560249090195 0.449188262224197 49.735767364502 5 21 -.MRTT#SFAK.V U
80
+ L gi|16129390|ref|NP_415948.1| Fake description
81
+ M 9 15 1022.09674242 0.382012128829956 0.448135405778885 52.3407211303711 5 16 K.DVKFGNDAR.V U
82
+ L gi|16131968|ref|NP_418567.1| Fake description
83
+ M 10 16 1022.09807242 0.398330867290497 0.436301857233047 49.735767364502 5 21 -.MRT#TSFAK.V U
84
+ L gi|16129390|ref|NP_415948.1| Fake description
85
+ S 24 24 1 0.0 TESLA 1422.02368164062 4142.11865234375 0.0 0
86
+ S 26 26 1 0.0 TESLA 444.820556640625 1576.70617675781 0.0 0
87
+ S 27 27 1 0.0 TESLA 393.008056640625 2896.16967773438 0.0 0
data/spec/testfiles/small2.sqt ADDED
@@ -0,0 +1,176 @@
1
+ H SQTGenerator mspire
2
+ H SQTGeneratorVersion 0.3.1
3
+ H Database C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
4
+ H FragmentMasses AVG
5
+ H PrecursorMasses AVG
6
+ H StartTime
7
+ H Alg-MSModel LCQ Deca XP
8
+ H DBLocusCount 4237
9
+ H Alg-FragMassTol 1.0000
10
+ H Alg-PreMassTol 25.0000
11
+ H Alg-IonSeries 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
12
+ H Alg-PreMassUnits ppm
13
+ H Alg-Enzyme Trypsin(KR/P) (2)
14
+ H Comment Created from Bioworks .srf file
15
+ H Comment ultrasmall created for testing
16
+ H DynamicMod M*=+15.99940
17
+ H DynamicMod STY#=+79.97990
18
+ S 2 2 1 0.0 TESLA 390.901550292969 2824.23608398438 0.0 0
19
+ S 3 3 1 0.0 TESLA 1121.98193359375 2875.275390625 0.0 28
20
+ M 1 2 1122.00110442 0.0 0.583871901035309 96.4032821655273 10 28 R.Y#LS#ENAHK.A U
21
+ L gi|16131875|ref|NP_418473.1|
22
+ M 2 1 1121.97977642 0.230631709098816 0.449212521314621 120.724304199219 11 32 -.MS#S#DADAHK.V U
23
+ L gi|16131941|ref|NP_418539.1|
24
+ M 3 5 1121.99941242 0.290755122900009 0.414108157157898 46.7291984558105 6 32 R.EDAAVT#LS#R.I U
25
+ L gi|16130949|ref|NP_417525.1|
26
+ M 4 7 1121.99941242 0.495447069406509 0.294594287872314 37.0694236755371 7 32 R.LDS#AS#EIAR.A U
27
+ L gi|16130103|ref|NP_416670.1|
28
+ M 5 8 1121.99941242 0.525885820388794 0.276821941137314 36.3679809570312 7 28 K.ET#QLT#DVR.I U
29
+ L gi|16130300|ref|NP_416869.1|
30
+ M 6 17 1122.00433442 0.590264618396759 0.23923297226429 14.6716089248657 5 32 R.T#WLGNS#AGR.I U
31
+ L gi|90111747|ref|NP_418809.4|
32
+ M 7 19 1122.00110442 0.608594477176666 0.228530704975128 13.1891889572144 5 28 R.SGKS#TY#YR.L U
33
+ L gi|16128299|ref|NP_414848.1|
34
+ M 8 21 1122.00110442 0.626765310764313 0.217921242117882 7.27399301528931 3 28 R.SGKS#T#YYR.L U
35
+ L gi|16128299|ref|NP_414848.1|
36
+ M 9 9 1122.00433442 0.64301460981369 0.208433717489243 31.834005355835 7 32 K.GS#Y#SHLAAR.Q U
37
+ L gi|16130520|ref|NP_417090.1|
38
+ M 10 18 1121.96119642 0.6480832695961 0.205474302172661 13.4426832199097 6 28 K.S#GNDLHY#R.G U
39
+ L gi|16128318|ref|NP_414867.1|
40
+ S 4 4 1 0.0 TESLA 1221.9462890625 3474.73559570312 0.0 0
41
+ S 6 6 1 0.0 TESLA 390.952697753906 2918.03833007812 0.0 0
42
+ S 8 8 1 0.0 TESLA 1222.1357421875 4032.162109375 0.0 37
43
+ M 1 3 1222.15888642 0.0 0.813828647136688 103.783157348633 11 36 K.LET#IEGS#KGK.V U
44
+ L gi|16128107|ref|NP_414656.1|
45
+ M 2 2 1222.12220842 0.0126136802136898 0.803563237190247 136.337341308594 14 32 R.RGKDVET#T#R.R U
46
+ L gi|16131703|ref|NP_418299.1|
47
+ M 3 6 1222.11574842 0.0502548851072788 0.772929787635803 68.2927017211914 11 36 K.DGT#LQALS#EK.W U
48
+ L gi|16129867|ref|NP_416430.1|
49
+ M 4 1 1222.16380842 0.376287251710892 0.507595300674438 158.161605834961 11 36 R.AGLT#PY#NVAR.K U
50
+ L gi|16128827|ref|NP_415380.1|
51
+ M 5 8 1222.11590242 0.490054965019226 0.41500785946846 65.2155609130859 10 32 R.DTPFFS#GY#K.M U
52
+ L gi|16131887|ref|NP_418485.1|
53
+ M 6 7 1222.16211642 0.533427715301514 0.379709869623184 66.9310073852539 9 32 R.S#SELT#QRLK.- U
54
+ L gi|16130352|ref|NP_416922.1|
55
+ M 7 4 1222.16211642 0.53839248418808 0.37566938996315 71.6616439819336 9 32 R.S#S#ELTQRLK.- U
56
+ L gi|16130352|ref|NP_416922.1|
57
+ M 8 12 1222.16211642 0.55070173740387 0.365651786327362 54.7290267944336 8 32 R.SS#ELT#QRLK.- U
58
+ L gi|16130352|ref|NP_416922.1|
59
+ M 9 14 1222.11590242 0.636659979820251 0.295696496963501 43.0032196044922 8 32 R.DT#PFFSGY#K.M U
60
+ L gi|16131887|ref|NP_418485.1|
61
+ M 10 9 1222.16380842 0.661910474300385 0.275146961212158 64.0063400268555 7 36 K.Y#SLT#AKGHGK.D U
62
+ L gi|16128068|ref|NP_414616.1|
63
+ S 10 10 1 0.0 TESLA 1121.7685546875 3271.79418945312 0.0 0
64
+ S 11 11 1 0.0 TESLA 370.779907226562 4604.28173828125 0.0 0
65
+ S 12 12 1 0.0 TESLA 1321.93017578125 3688.99169921875 0.0 0
66
+ S 14 14 1 0.0 TESLA 444.695190429688 1618.59875488281 0.0 0
67
+ S 15 15 1 0.0 TESLA 354.802124023438 2956.32495117188 0.0 0
68
+ S 16 16 1 0.0 TESLA 1321.94677734375 3914.71069335938 0.0 0
69
+ S 18 18 1 0.0 TESLA 1021.91040039062 2870.08032226562 0.0 17
70
+ M 1 3 1021.92467642 0.0 0.399370312690735 42.8986206054688 5 24 K.VDY#T#HVK.L U
71
+ L gi|16130545|ref|NP_417116.1|
72
+ M 2 4 1021.92944442 0.184633135795593 0.325633317232132 19.0969104766846 4 28 K.GRT#T#TLGR.G U
73
+ L gi|16131850|ref|NP_418448.1|
74
+ M 3 1 1021.89878842 0.318098336458206 0.272331267595291 101.136024475098 7 21 R.KNFSDT#DD.- U
75
+ L gi|90111696|ref|NP_418585.4|
76
+ M 4 8 1021.92944442 0.341504245996475 0.262983649969101 12.7322721481323 3 28 K.GRT#TT#LGR.G U
77
+ L gi|16131850|ref|NP_418448.1|
78
+ M 5 8 1021.92944442 0.363083690404892 0.25436544418335 12.7322721481323 3 28 K.GRTT#T#LGR.G U
79
+ L gi|16131850|ref|NP_418448.1|
80
+ M 6 10 1021.92944442 0.643937468528748 0.142200797796249 8.3918981552124 3 28 R.AT#RVTGT#R.A U
81
+ L gi|90111474|ref|NP_417134.2|
82
+ M 7 7 1021.92944442 0.660101413726807 0.135745406150818 16.1839351654053 4 28 R.QT#S#GRKGK.G U
83
+ L gi|90111241|ref|NP_415798.2|
84
+ M 8 11 1021.92467642 0.77150171995163 0.0912554189562798 7.69776201248169 2 24 R.HFT#DIT#K.Q U
85
+ L gi|16128760|ref|NP_415313.1|
86
+ M 9 5 1021.92298442 0.801752269268036 0.0791742652654648 17.7059764862061 4 32 R.DGT#IALS#GK.T U
87
+ L gi|16129472|ref|NP_416030.1|
88
+ M 10 2 1021.89878842 0.868551790714264 0.0524965040385723 90.8520126342773 7 21 R.KNFS#DTDD.- U
89
+ L gi|90111696|ref|NP_418585.4|
90
+ S 19 19 1 0.0 TESLA 1123.43481445312 3197.35522460938 0.0 10
91
+ M 1 1 1123.42062742 0.0 0.828362166881561 122.591445922852 7 16 K.MLPHIPQMR.V U
92
+ L gi|16130653|ref|NP_417226.1|
93
+ M 2 2 1123.41676142 0.557557225227356 0.366502851247787 42.6177139282227 5 18 R.LKGKLHVISK.R U
94
+ L gi|16128015|ref|NP_414562.1|
95
+ L gi|16128249|ref|NP_414798.1|
96
+ L gi|16128259|ref|NP_414808.1|
97
+ L gi|16128954|ref|NP_415508.1|
98
+ L gi|16129845|ref|NP_416407.1|
99
+ L gi|16131317|ref|NP_417902.1|
100
+ M 3 4 1123.41570542 0.951010406017303 0.0405811481177807 3.40660500526428 2 20 R.VSAGMTAKVKM.- U
101
+ L gi|16131722|ref|NP_418318.1|
102
+ M 4 3 1123.41676142 0.966903269290924 0.0274160970002413 6.50634431838989 3 20 K.GIKALIAAPLR.I U
103
+ L gi|16128083|ref|NP_414632.1|
104
+ S 20 20 1 0.0 TESLA 444.8203125 1524.58166503906 0.0 0
105
+ S 22 22 1 0.0 TESLA 358.580200195312 4363.13525390625 0.0 0
106
+ S 23 23 1 0.0 TESLA 347.777587890625 4914.42041015625 0.0 0
107
+ S 24 24 1 0.0 TESLA 371.997375488281 4020.958984375 0.0 0
108
+ S 26 26 1 0.0 TESLA 1021.99768066406 2683.08032226562 0.0 13
109
+ M 1 1 1022.00856642 0.0 0.4293093085289 79.3525314331055 7 21 -.MS#DQFDAK.A U
110
+ L gi|90111354|ref|NP_416423.4|
111
+ M 2 2 1022.01179642 0.016194524243474 0.422356843948364 35.1557731628418 5 18 K.DMNDKY#R.E U
112
+ L gi|49176314|ref|YP_026204.1|
113
+ M 3 3 1022.01179642 0.579394161701202 0.180570006370544 33.1019477844238 5 21 R.TMEY#GNAR.D U
114
+ L gi|49176090|ref|YP_025300.1|
115
+ M 4 4 1022.01179642 0.58598518371582 0.177740409970284 18.9654598236084 4 21 R.T#MEYGNAR.D U
116
+ L gi|49176090|ref|YP_025300.1|
117
+ M 5 5 1022.01176642 0.813580214977264 0.0800317376852036 12.4701271057129 4 21 K.AGM*AEY#QR.R U
118
+ L gi|16129800|ref|NP_416361.1|
119
+ M 6 10 1021.99152442 0.839166581630707 0.069047287106514 5.62248277664185 2 21 R.RIHS#ADDK.S U
120
+ L gi|16130546|ref|NP_417117.1|
121
+ M 7 8 1021.99152442 0.84443324804306 0.0667862594127655 10.4367046356201 4 21 R.HVNSES#LR.K U
122
+ L gi|16130312|ref|NP_416881.1|
123
+ M 8 11 1021.98506442 0.897791266441345 0.0438791699707508 4.91967248916626 2 24 K.T#ASASFTEK.C U
124
+ L gi|16129613|ref|NP_416172.1|
125
+ M 9 11 1021.98506442 0.925069570541382 0.0321683175861835 4.91967248916626 2 24 K.TAS#ASFTEK.C U
126
+ L gi|16129613|ref|NP_416172.1|
127
+ M 10 6 1021.98506442 0.930912971496582 0.0296596921980381 11.1198310852051 3 24 K.TASASFT#EK.C U
128
+ L gi|16129613|ref|NP_416172.1|
129
+ S 27 27 1 0.0 TESLA 844.472412109375 3693.63232421875 0.0 0
130
+ S 28 30 1 0.0 TESLA 361.102355957031 4481.24462890625 0.0 0
131
+ S 31 31 1 0.0 TESLA 392.985412597656 2787.99877929688 0.0 0
132
+ S 32 32 2 0.0 TESLA 716.18559446375 4379.787109375 0.0 0
133
+ S 32 32 3 0.0 TESLA 1073.77475338063 4379.787109375 0.0 0
134
+ S 34 34 2 0.0 TESLA 650.821947002813 3247.47631835938 0.0 17
135
+ M 1 2 650.81424342 0.0 0.285814881324768 16.3779792785645 2 8 -.M*SKIR.V U
136
+ L gi|16129835|ref|NP_416397.1|
137
+ M 2 3 650.81424342 0.00219042110256851 0.28518882393837 12.5 1 8 K.M*SLRK.L U
138
+ L gi|16132129|ref|NP_418728.1|
139
+ M 3 2 650.81424342 0.440997421741486 0.159771263599396 16.3779792785645 2 8 R.SM*KLR.V U
140
+ L gi|16130956|ref|NP_417532.1|
141
+ M 4 2 650.81424342 0.578712046146393 0.120410367846489 16.3779792785645 2 8 -.M*KSLR.L U
142
+ L gi|16130357|ref|NP_416927.1|
143
+ M 5 1 650.83777542 0.626044392585754 0.106882072985172 48.4102210998535 3 10 R.VGMGMR.M U
144
+ L gi|16131833|ref|NP_418431.1|
145
+ M 6 6 650.81424342 0.912068605422974 0.0251320991665125 2.67464756965637 1 8 -.M*TKVR.N U
146
+ L gi|16132219|ref|NP_418819.1|
147
+ M 7 4 650.81101342 0.913021624088287 0.0248597171157598 4.11436176300049 1 8 K.IKKDM*.- U
148
+ L gi|16131382|ref|NP_417967.1|
149
+ S 34 34 3 0.0 TESLA 975.729282189219 3247.47631835938 0.0 4
150
+ M 1 1 975.70918642 0.0 0.336968153715134 123.62523651123 13 50 K.T#S#S#ERR.V U
151
+ L gi|90111273|ref|NP_415952.2|
152
+ M 2 2 975.70918642 0.855341613292694 0.048745259642601 45.2420883178711 8 50 K.DS#T#RT#R.C U
153
+ L gi|16128258|ref|NP_414807.1|
154
+ L gi|16132076|ref|NP_418675.1|
155
+ S 35 35 2 0.0 TESLA 629.121995830938 3744.17602539062 0.0 0
156
+ S 35 35 3 0.0 TESLA 943.179355431406 3744.17602539062 0.0 12
157
+ M 1 3 943.16893942 0.0 0.807636499404907 62.7209167480469 5 28 R.EILKVKGR.M U
158
+ L gi|16128422|ref|NP_414971.1|
159
+ M 2 5 943.18767342 0.376235246658325 0.503775238990784 33.4877433776855 4 28 R.ISMGLFFK.Y U
160
+ L gi|16129739|ref|NP_416299.1|
161
+ M 3 1 943.19244142 0.40588042140007 0.479832679033279 82.5799865722656 6 28 K.LQLKPGMR.V U
162
+ L gi|16129619|ref|NP_416178.1|
163
+ M 4 8 943.19132542 0.661087512969971 0.273718118667603 15.2403078079224 3 28 -.M*LVSCAM*R.L U
164
+ L gi|16128439|ref|NP_414988.1|
165
+ M 5 6 943.16417142 0.723082005977631 0.223649099469185 22.7307662963867 4 28 R.EIPFIPVK.S U
166
+ L gi|16130724|ref|NP_417297.1|
167
+ S 36 36 2 0.0 TESLA 602.796678448125 3761.94702148438 0.0 2
168
+ M 1 1 602.78925142 0.0 0.0683688968420029 2.98955655097961 1 8 R.KLLTK.Y U
169
+ L gi|16129799|ref|NP_416360.1|
170
+ L gi|16130740|ref|NP_417313.1|
171
+ S 36 36 3 0.0 TESLA 903.691379357188 3761.94702148438 0.0 2
172
+ M 1 1 903.68287642 0.0 0.355157345533371 145.232284545898 12 60 R.S#S#ALAS#K.A U
173
+ L gi|16128027|ref|NP_414574.1|
174
+ M 2 2 903.68287642 0.844804406166077 0.0551188476383686 65.4463500976562 8 50 K.T#IS#S#QK.K U
175
+ L gi|16130154|ref|NP_416721.1|
176
+