mspire 0.4.9 → 0.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (255) hide show
  1. data/README +27 -17
  2. data/changelog.txt +31 -62
  3. data/lib/ms/calc.rb +32 -0
  4. data/lib/ms/data/interleaved.rb +60 -0
  5. data/lib/ms/data/lazy_io.rb +73 -0
  6. data/lib/ms/data/lazy_string.rb +15 -0
  7. data/lib/ms/data/simple.rb +59 -0
  8. data/lib/ms/data/transposed.rb +41 -0
  9. data/lib/ms/data.rb +57 -0
  10. data/lib/ms/format/format_error.rb +12 -0
  11. data/lib/ms/spectrum.rb +25 -384
  12. data/lib/ms/support/binary_search.rb +126 -0
  13. data/lib/ms.rb +10 -10
  14. metadata +38 -350
  15. data/INSTALL +0 -58
  16. data/README.rdoc +0 -18
  17. data/Rakefile +0 -330
  18. data/bin/aafreqs.rb +0 -23
  19. data/bin/bioworks2excel.rb +0 -14
  20. data/bin/bioworks_to_pepxml.rb +0 -148
  21. data/bin/bioworks_to_pepxml_gui.rb +0 -225
  22. data/bin/fasta_shaker.rb +0 -5
  23. data/bin/filter_and_validate.rb +0 -5
  24. data/bin/gi2annot.rb +0 -14
  25. data/bin/id_class_anal.rb +0 -112
  26. data/bin/id_precision.rb +0 -172
  27. data/bin/ms_to_lmat.rb +0 -67
  28. data/bin/pepproph_filter.rb +0 -16
  29. data/bin/prob_validate.rb +0 -6
  30. data/bin/protein_summary.rb +0 -6
  31. data/bin/protxml2prots_peps.rb +0 -32
  32. data/bin/raw_to_mzXML.rb +0 -55
  33. data/bin/run_percolator.rb +0 -122
  34. data/bin/sqt_group.rb +0 -26
  35. data/bin/srf_group.rb +0 -27
  36. data/bin/srf_to_sqt.rb +0 -40
  37. data/lib/align/chams.rb +0 -78
  38. data/lib/align.rb +0 -154
  39. data/lib/archive/targz.rb +0 -94
  40. data/lib/bsearch.rb +0 -120
  41. data/lib/core_extensions.rb +0 -16
  42. data/lib/fasta.rb +0 -626
  43. data/lib/gi.rb +0 -124
  44. data/lib/group_by.rb +0 -10
  45. data/lib/index_by.rb +0 -11
  46. data/lib/merge_deep.rb +0 -21
  47. data/lib/ms/converter/mzxml.rb +0 -77
  48. data/lib/ms/gradient_program.rb +0 -170
  49. data/lib/ms/msrun.rb +0 -244
  50. data/lib/ms/msrun_index.rb +0 -108
  51. data/lib/ms/parser/mzdata/axml.rb +0 -67
  52. data/lib/ms/parser/mzdata/dom.rb +0 -175
  53. data/lib/ms/parser/mzdata/libxml.rb +0 -7
  54. data/lib/ms/parser/mzdata.rb +0 -31
  55. data/lib/ms/parser/mzxml/axml.rb +0 -70
  56. data/lib/ms/parser/mzxml/dom.rb +0 -182
  57. data/lib/ms/parser/mzxml/hpricot.rb +0 -253
  58. data/lib/ms/parser/mzxml/libxml.rb +0 -19
  59. data/lib/ms/parser/mzxml/regexp.rb +0 -122
  60. data/lib/ms/parser/mzxml/rexml.rb +0 -72
  61. data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
  62. data/lib/ms/parser/mzxml.rb +0 -282
  63. data/lib/ms/parser.rb +0 -108
  64. data/lib/ms/precursor.rb +0 -25
  65. data/lib/ms/scan.rb +0 -81
  66. data/lib/mspire.rb +0 -4
  67. data/lib/pi_zero.rb +0 -244
  68. data/lib/qvalue.rb +0 -161
  69. data/lib/roc.rb +0 -187
  70. data/lib/sample_enzyme.rb +0 -160
  71. data/lib/scan_i.rb +0 -21
  72. data/lib/spec_id/aa_freqs.rb +0 -170
  73. data/lib/spec_id/bioworks.rb +0 -497
  74. data/lib/spec_id/digestor.rb +0 -138
  75. data/lib/spec_id/mass.rb +0 -179
  76. data/lib/spec_id/parser/proph.rb +0 -335
  77. data/lib/spec_id/precision/filter/cmdline.rb +0 -218
  78. data/lib/spec_id/precision/filter/interactive.rb +0 -134
  79. data/lib/spec_id/precision/filter/output.rb +0 -148
  80. data/lib/spec_id/precision/filter.rb +0 -637
  81. data/lib/spec_id/precision/output.rb +0 -60
  82. data/lib/spec_id/precision/prob/cmdline.rb +0 -160
  83. data/lib/spec_id/precision/prob/output.rb +0 -94
  84. data/lib/spec_id/precision/prob.rb +0 -249
  85. data/lib/spec_id/proph/pep_summary.rb +0 -104
  86. data/lib/spec_id/proph/prot_summary.rb +0 -484
  87. data/lib/spec_id/proph.rb +0 -4
  88. data/lib/spec_id/protein_summary.rb +0 -489
  89. data/lib/spec_id/sequest/params.rb +0 -316
  90. data/lib/spec_id/sequest/pepxml.rb +0 -1458
  91. data/lib/spec_id/sequest.rb +0 -33
  92. data/lib/spec_id/sqt.rb +0 -349
  93. data/lib/spec_id/srf.rb +0 -973
  94. data/lib/spec_id.rb +0 -778
  95. data/lib/spec_id_xml.rb +0 -99
  96. data/lib/transmem/phobius.rb +0 -147
  97. data/lib/transmem/toppred.rb +0 -368
  98. data/lib/transmem.rb +0 -157
  99. data/lib/validator/aa.rb +0 -48
  100. data/lib/validator/aa_est.rb +0 -112
  101. data/lib/validator/background.rb +0 -77
  102. data/lib/validator/bias.rb +0 -95
  103. data/lib/validator/cmdline.rb +0 -431
  104. data/lib/validator/decoy.rb +0 -107
  105. data/lib/validator/digestion_based.rb +0 -70
  106. data/lib/validator/probability.rb +0 -51
  107. data/lib/validator/prot_from_pep.rb +0 -234
  108. data/lib/validator/q_value.rb +0 -32
  109. data/lib/validator/transmem.rb +0 -272
  110. data/lib/validator/true_pos.rb +0 -46
  111. data/lib/validator.rb +0 -197
  112. data/lib/xml.rb +0 -38
  113. data/lib/xml_style_parser.rb +0 -119
  114. data/lib/xmlparser_wrapper.rb +0 -19
  115. data/release_notes.txt +0 -2
  116. data/script/compile_and_plot_smriti_final.rb +0 -97
  117. data/script/create_little_pepxml.rb +0 -61
  118. data/script/degenerate_peptides.rb +0 -47
  119. data/script/estimate_fpr_by_cysteine.rb +0 -226
  120. data/script/extract_gradient_programs.rb +0 -56
  121. data/script/find_cysteine_background.rb +0 -137
  122. data/script/genuine_tps_and_probs.rb +0 -136
  123. data/script/get_apex_values_rexml.rb +0 -44
  124. data/script/histogram_probs.rb +0 -61
  125. data/script/mascot_fix_pepxml.rb +0 -123
  126. data/script/msvis.rb +0 -42
  127. data/script/mzXML2timeIndex.rb +0 -25
  128. data/script/peps_per_bin.rb +0 -67
  129. data/script/prep_dir.rb +0 -121
  130. data/script/simple_protein_digestion.rb +0 -27
  131. data/script/smriti_final_analysis.rb +0 -103
  132. data/script/sqt_to_meta.rb +0 -24
  133. data/script/top_hit_per_scan.rb +0 -67
  134. data/script/toppred_to_yaml.rb +0 -47
  135. data/script/tpp_installer.rb +0 -249
  136. data/specs/align_spec.rb +0 -79
  137. data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
  138. data/specs/bin/fasta_shaker_spec.rb +0 -259
  139. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
  140. data/specs/bin/filter_and_validate_spec.rb +0 -180
  141. data/specs/bin/ms_to_lmat_spec.rb +0 -34
  142. data/specs/bin/prob_validate_spec.rb +0 -86
  143. data/specs/bin/protein_summary_spec.rb +0 -14
  144. data/specs/fasta_spec.rb +0 -354
  145. data/specs/gi_spec.rb +0 -22
  146. data/specs/load_bin_path.rb +0 -7
  147. data/specs/merge_deep_spec.rb +0 -13
  148. data/specs/ms/gradient_program_spec.rb +0 -77
  149. data/specs/ms/msrun_spec.rb +0 -498
  150. data/specs/ms/parser_spec.rb +0 -92
  151. data/specs/ms/spectrum_spec.rb +0 -87
  152. data/specs/pi_zero_spec.rb +0 -115
  153. data/specs/qvalue_spec.rb +0 -39
  154. data/specs/roc_spec.rb +0 -251
  155. data/specs/rspec_autotest.rb +0 -149
  156. data/specs/sample_enzyme_spec.rb +0 -126
  157. data/specs/spec_helper.rb +0 -135
  158. data/specs/spec_id/aa_freqs_spec.rb +0 -52
  159. data/specs/spec_id/bioworks_spec.rb +0 -148
  160. data/specs/spec_id/digestor_spec.rb +0 -75
  161. data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
  162. data/specs/spec_id/precision/filter/output_spec.rb +0 -31
  163. data/specs/spec_id/precision/filter_spec.rb +0 -246
  164. data/specs/spec_id/precision/prob_spec.rb +0 -44
  165. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  166. data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
  167. data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
  168. data/specs/spec_id/protein_summary_spec.rb +0 -189
  169. data/specs/spec_id/sequest/params_spec.rb +0 -68
  170. data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
  171. data/specs/spec_id/sequest_spec.rb +0 -38
  172. data/specs/spec_id/sqt_spec.rb +0 -246
  173. data/specs/spec_id/srf_spec.rb +0 -172
  174. data/specs/spec_id/srf_spec_helper.rb +0 -139
  175. data/specs/spec_id_helper.rb +0 -33
  176. data/specs/spec_id_spec.rb +0 -366
  177. data/specs/spec_id_xml_spec.rb +0 -33
  178. data/specs/transmem/phobius_spec.rb +0 -425
  179. data/specs/transmem/toppred_spec.rb +0 -298
  180. data/specs/transmem_spec.rb +0 -60
  181. data/specs/transmem_spec_shared.rb +0 -64
  182. data/specs/validator/aa_est_spec.rb +0 -66
  183. data/specs/validator/aa_spec.rb +0 -40
  184. data/specs/validator/background_spec.rb +0 -67
  185. data/specs/validator/bias_spec.rb +0 -122
  186. data/specs/validator/decoy_spec.rb +0 -51
  187. data/specs/validator/fasta_helper.rb +0 -26
  188. data/specs/validator/prot_from_pep_spec.rb +0 -141
  189. data/specs/validator/transmem_spec.rb +0 -146
  190. data/specs/validator/true_pos_spec.rb +0 -58
  191. data/specs/validator_helper.rb +0 -33
  192. data/specs/xml_spec.rb +0 -12
  193. data/test_files/000_pepxml18_small.xml +0 -206
  194. data/test_files/020a.mzXML.timeIndex +0 -4710
  195. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
  196. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
  197. data/test_files/4-03-03_small-prot.xml +0 -321
  198. data/test_files/4-03-03_small.xml +0 -3876
  199. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  200. data/test_files/bioworks-3.3_10prots.xml +0 -5999
  201. data/test_files/bioworks31.params +0 -77
  202. data/test_files/bioworks32.params +0 -62
  203. data/test_files/bioworks33.params +0 -63
  204. data/test_files/bioworks_single_run_small.xml +0 -7237
  205. data/test_files/bioworks_small.fasta +0 -212
  206. data/test_files/bioworks_small.params +0 -63
  207. data/test_files/bioworks_small.phobius +0 -109
  208. data/test_files/bioworks_small.toppred.out +0 -2847
  209. data/test_files/bioworks_small.xml +0 -5610
  210. data/test_files/bioworks_with_INV_small.xml +0 -3753
  211. data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
  212. data/test_files/corrupted_900.srf +0 -0
  213. data/test_files/head_of_7MIX.srf +0 -0
  214. data/test_files/interact-opd1_mods_small-prot.xml +0 -304
  215. data/test_files/messups.fasta +0 -297
  216. data/test_files/opd1/000.my_answer.100lines.xml +0 -101
  217. data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
  218. data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
  219. data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
  220. data/test_files/opd1/000_020-prot.png +0 -0
  221. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
  222. data/test_files/opd1/000_020_3prots-prot.xml +0 -62
  223. data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
  224. data/test_files/opd1/sequest.3.1.params +0 -77
  225. data/test_files/opd1/sequest.3.2.params +0 -62
  226. data/test_files/opd1/twenty_scans.mzXML +0 -418
  227. data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
  228. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  229. data/test_files/opd1/twenty_scans_answ.lmata +0 -9
  230. data/test_files/opd1_020_beginning.RAW +0 -0
  231. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
  232. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
  233. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
  234. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
  235. data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
  236. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
  237. data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
  238. data/test_files/pepproph_small.xml +0 -4691
  239. data/test_files/phobius.small.noheader.txt +0 -50
  240. data/test_files/phobius.small.small.txt +0 -53
  241. data/test_files/s01_anC1_ld020mM.key.txt +0 -25
  242. data/test_files/s01_anC1_ld020mM.meth +0 -0
  243. data/test_files/small.fasta +0 -297
  244. data/test_files/small.sqt +0 -87
  245. data/test_files/smallraw.RAW +0 -0
  246. data/test_files/tf_bioworks2excel.bioXML +0 -14340
  247. data/test_files/tf_bioworks2excel.txt.actual +0 -1035
  248. data/test_files/toppred.small.out +0 -416
  249. data/test_files/toppred.xml.out +0 -318
  250. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
  251. data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
  252. data/test_files/yeast_gly_small-prot.xml +0 -265
  253. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
  254. data/test_files/yeast_gly_small.xml +0 -3807
  255. data/test_files/yeast_gly_small2.parentTimes +0 -6
data/test_files/bioworks31.params DELETED
@@ -1,77 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 1.5000
5
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
6
- fragment_ion_tolerance = 0.0000 ; leave at 0.0 unless you have real poor data
7
- num_output_lines = 10 ; # peptide results to show
8
- num_results = 500 ; # results to store
9
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
10
- show_fragment_ions = 1 ; 0=no, 1=yes
11
- print_duplicate_references = 40 ; 0=no, 1=yes
12
- enzyme_number = 1
13
- max_num_differential_AA_per_mod = 4 ; max # of modified AA per diff. mod in a peptide
14
- diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
15
- term_diff_search_options = 0.0000 0.0000
16
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
17
- mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
18
- mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
19
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
20
- remove_precursor_peak = 0 ; 0=no, 1=yes
21
- ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
22
- max_num_internal_cleavage_sites = 2 ; maximum value is 5
23
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
24
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
25
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
26
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
27
- create_output_files = 1 ; 0=no, 1=yes
28
- partial_sequence =
29
- sequence_header_filter =
30
-
31
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
32
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
33
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
34
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
35
- add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146
36
- add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711
37
- add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303
38
- add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276
39
- add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841
40
- add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768
41
- add_C_Cysteine = 0.0000 ; added to C - avg. 103.1388, mono. 103.00919
42
- add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406
43
- add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406
44
- add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
45
- add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
46
- add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
47
- add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
48
- add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
49
- add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
50
- add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
51
- add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
52
- add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
53
- add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
54
- add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
55
- add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
56
- add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
57
- add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
58
- add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931
59
-
60
- [SEQUEST_ENZYME_INFO]
61
- 0. No_Enzyme 0 - -
62
- 1. Trypsin 1 KR -
63
- 2. Trypsin(KRLNH) 1 KRLNH -
64
- 3. Chymotrypsin 1 FWYL -
65
- 4. Chymotrypsin(FWY) 1 FWY P
66
- 5. Clostripain 1 R -
67
- 6. Cyanogen_Bromide 1 M -
68
- 7. IodosoBenzoate 1 W -
69
- 8. Proline_Endopept 1 P -
70
- 9. Staph_Protease 1 E -
71
- 10. Trypsin_K 1 K P
72
- 11. Trypsin_R 1 R P
73
- 12. GluC 1 ED -
74
- 13. LysC 1 K -
75
- 14. AspN 0 D -
76
- 15. Elastase 1 ALIV P
77
- 16. Elastase/Tryp/Chymo 1 ALIVKRWFY P
data/test_files/bioworks32.params DELETED
@@ -1,62 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 1.4000
5
- peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
6
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
7
- fragment_ion_tolerance = 1.0000 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
8
- num_output_lines = 10 ; # peptide results to show
9
- num_results = 250 ; # results to store
10
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
11
- show_fragment_ions = 0 ; 0=no, 1=yes
12
- print_duplicate_references = 40 ; number of duplicate references reported
13
- enzyme_info = Trypsin(KR/P) 1 1 KR P
14
- max_num_differential_per_peptide = 1 ; max # of diff. mod in a peptide
15
- diff_search_options = 0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
16
- term_diff_search_options = 0.000000 0.000000
17
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
18
- mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
19
- mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
20
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
21
- remove_precursor_peak = 0 ; 0=no, 1=yes
22
- 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
24
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
25
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
26
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
27
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
28
- partial_sequence =
29
- sequence_header_filter =
30
- digest_mass_range = 600.0 3500.0
31
-
32
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
33
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
34
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
35
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
36
- add_G_Glycine = 0.0000 ; added to G
37
- add_A_Alanine = 0.0000 ; added to A
38
- add_S_Serine = 0.0000 ; added to S
39
- add_P_Proline = 0.0000 ; added to P
40
- add_V_Valine = 0.0000 ; added to V
41
- add_T_Threonine = 0.0000 ; added to T
42
- add_C_Cysteine = 0.0000 ; added to C
43
- add_L_Leucine = 0.0000 ; added to L
44
- add_I_Isoleucine = 0.0000 ; added to I
45
- add_X_LorI = 0.0000 ; added to X
46
- add_N_Asparagine = 0.0000 ; added to N
47
- add_O_Ornithine = 0.0000 ; added to O
48
- add_B_avg_NandD = 0.0000 ; added to B
49
- add_D_Aspartic_Acid = 0.0000 ; added to D
50
- add_Q_Glutamine = 0.0000 ; added to Q
51
- add_K_Lysine = 0.0000 ; added to K
52
- add_Z_avg_QandE = 0.0000 ; added to Z
53
- add_E_Glutamic_Acid = 0.0000 ; added to E
54
- add_M_Methionine = 0.0000 ; added to M
55
- add_H_Histidine = 0.0000 ; added to H
56
- add_F_Phenylalanine = 0.0000 ; added to F
57
- add_R_Arginine = 0.0000 ; added to R
58
- add_Y_Tyrosine = 0.0000 ; added to Y
59
- add_W_Tryptophan = 0.0000 ; added to W
60
- add_J_user_amino_acid = 0.0000 ; added to J
61
- add_U_user_amino_acid = 0.0000 ; added to U
62
-
data/test_files/bioworks33.params DELETED
@@ -1,63 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\yeast.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 2.0000
5
- peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
6
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
7
- 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
9
- 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
14
- 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
17
- term_diff_search_options = 0.0000 0.0000
18
- 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
40
- add_P_Proline = 0.0000 ; added to P
41
- add_V_Valine = 0.0000 ; added to V
42
- add_T_Threonine = 0.0000 ; added to T
43
- add_C_Cysteine = 0.0000 ; added to C
44
- add_L_Leucine = 0.0000 ; added to L
45
- add_I_Isoleucine = 0.0000 ; added to I
46
- add_X_LorI = 0.0000 ; added to X
47
- add_N_Asparagine = 0.0000 ; added to N
48
- 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
-