mspire 0.4.9 → 0.5.0

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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/phobius.small.noheader.txt DELETED
@@ -1,50 +0,0 @@
1
- gi|16127995|ref|NP_414542.1| 0 0 i
2
- gi|16127996|ref|NP_414543.1| 0 0 i
3
- gi|16127997|ref|NP_414544.1| 0 0 i
4
- gi|16127998|ref|NP_414545.1| 0 0 i
5
- gi|16127999|ref|NP_414546.1| 0 Y n6-17c23/24o
6
- gi|16128000|ref|NP_414547.1| 0 0 i
7
- gi|16128001|ref|NP_414548.1| 9 0 o12-30i68-87o93-116i137-156o176-194i206-228o297-321i342-370o414-438i
8
- gi|16128002|ref|NP_414549.1| 0 0 i
9
- gi|16128003|ref|NP_414550.1| 0 0 i
10
- gi|16128004|ref|NP_414551.1| 6 0 i12-31o37-56i63-84o96-116i123-143o149-169i
11
- gi|16128005|ref|NP_414552.1| 0 0 i
12
- gi|90111078|ref|NP_414553.2| 0 0 i
13
- gi|16128007|ref|NP_414554.1| 0 Y n4-15c23/24o
14
- gi|16128008|ref|NP_414555.1| 0 0 i
15
- gi|16128009|ref|NP_414556.1| 0 0 i
16
- gi|16128010|ref|NP_414557.1| 0 0 i
17
- gi|16128011|ref|NP_414558.1| 0 0 i
18
- gi|16128012|ref|NP_414559.1| 1 0 i25-44o
19
- gi|49175991|ref|YP_025292.1| 0 Y n8-16c21/22o
20
- gi|16128013|ref|NP_414560.1| 11 0 i12-39o59-79i91-114o126-145i154-175o181-200i207-238o258-276i288-312o324-351i363-380o
21
- gi|16128014|ref|NP_414561.1| 0 0 i
22
- gi|16128015|ref|NP_414562.1| 0 0 i
23
- gi|16128016|ref|NP_414563.1| 0 0 i
24
- gi|16128017|ref|NP_414564.1| 0 0 i
25
- gi|16128018|ref|NP_414565.1| 0 0 i
26
- gi|16128019|ref|NP_414566.1| 0 0 i
27
- gi|16128020|ref|NP_414567.1| 0 0 i
28
- gi|16128021|ref|NP_414568.1| 4 0 i12-31o70-88i100-117o137-157i
29
- gi|16128022|ref|NP_414569.1| 0 0 i
30
- gi|16128023|ref|NP_414570.1| 0 0 i
31
- gi|16128024|ref|NP_414571.1| 0 0 i
32
- gi|16128025|ref|NP_414572.1| 0 0 i
33
- gi|16128026|ref|NP_414573.1| 0 0 i
34
- gi|16128027|ref|NP_414574.1| 0 Y n9-16c21/22o
35
- gi|90111079|ref|NP_414576.4| 0 0 i
36
- gi|90111080|ref|NP_414577.2| 0 0 i
37
- gi|16128030|ref|NP_414578.1| 0 0 i
38
- gi|49175993|ref|NP_414579.3| 0 0 i
39
- gi|16128032|ref|NP_414580.1| 0 0 i
40
- gi|16128033|ref|NP_414581.1| 0 0 i
41
- gi|16128034|ref|NP_414582.1| 12 0 i12-30o50-71i91-116o145-163i195-216o228-251i263-286o318-335i347-366o406-425i446-466o472-495i
42
- gi|90111081|ref|NP_414583.2| 0 0 i
43
- gi|16128036|ref|NP_414584.1| 0 0 i
44
- gi|16128037|ref|NP_414585.1| 0 Y n8-19c25/26o
45
- gi|16128038|ref|NP_414586.1| 0 0 i
46
- gi|16128039|ref|NP_414587.1| 12 0 i20-42o54-74i86-104o110-132i144-166o172-193i242-263o283-303i310-329o335-358i370-390o402-421i
47
- gi|16128040|ref|NP_414588.1| 0 0 i
48
- gi|16128041|ref|NP_414589.1| 13 0 o6-24i31-49o55-72i84-111o117-135i147-169o181-202i214-233o239-258i270-290o296-315i327-348o360-378i
49
- gi|16128042|ref|NP_414590.1| 0 Y n2-10c15/16o
50
- gi|16128043|ref|NP_414591.1| 0 0 i
data/test_files/phobius.small.small.txt DELETED
@@ -1,53 +0,0 @@
1
- Phobius prediction
2
-
3
- SEQENCE ID TM SP PREDICTION
4
- gi|16127995|ref|NP_414542.1| 0 0 i
5
- gi|16127996|ref|NP_414543.1| 0 0 i
6
- gi|16127997|ref|NP_414544.1| 0 0 i
7
- gi|16127998|ref|NP_414545.1| 0 0 i
8
- gi|16127999|ref|NP_414546.1| 0 Y n6-17c23/24o
9
- gi|16128000|ref|NP_414547.1| 0 0 i
10
- gi|16128001|ref|NP_414548.1| 9 0 o12-30i68-87o93-116i137-156o176-194i206-228o297-321i342-370o414-438i
11
- gi|16128002|ref|NP_414549.1| 0 0 i
12
- gi|16128003|ref|NP_414550.1| 0 0 i
13
- gi|16128004|ref|NP_414551.1| 6 0 i12-31o37-56i63-84o96-116i123-143o149-169i
14
- gi|16128005|ref|NP_414552.1| 0 0 i
15
- gi|90111078|ref|NP_414553.2| 0 0 i
16
- gi|16128007|ref|NP_414554.1| 0 Y n4-15c23/24o
17
- gi|16128008|ref|NP_414555.1| 0 0 i
18
- gi|16128009|ref|NP_414556.1| 0 0 i
19
- gi|16128010|ref|NP_414557.1| 0 0 i
20
- gi|16128011|ref|NP_414558.1| 0 0 i
21
- gi|16128012|ref|NP_414559.1| 1 0 i25-44o
22
- gi|49175991|ref|YP_025292.1| 0 Y n8-16c21/22o
23
- gi|16128013|ref|NP_414560.1| 11 0 i12-39o59-79i91-114o126-145i154-175o181-200i207-238o258-276i288-312o324-351i363-380o
24
- gi|16128014|ref|NP_414561.1| 0 0 i
25
- gi|16128015|ref|NP_414562.1| 0 0 i
26
- gi|16128016|ref|NP_414563.1| 0 0 i
27
- gi|16128017|ref|NP_414564.1| 0 0 i
28
- gi|16128018|ref|NP_414565.1| 0 0 i
29
- gi|16128019|ref|NP_414566.1| 0 0 i
30
- gi|16128020|ref|NP_414567.1| 0 0 i
31
- gi|16128021|ref|NP_414568.1| 4 0 i12-31o70-88i100-117o137-157i
32
- gi|16128022|ref|NP_414569.1| 0 0 i
33
- gi|16128023|ref|NP_414570.1| 0 0 i
34
- gi|16128024|ref|NP_414571.1| 0 0 i
35
- gi|16128025|ref|NP_414572.1| 0 0 i
36
- gi|16128026|ref|NP_414573.1| 0 0 i
37
- gi|16128027|ref|NP_414574.1| 0 Y n9-16c21/22o
38
- gi|90111079|ref|NP_414576.4| 0 0 i
39
- gi|90111080|ref|NP_414577.2| 0 0 i
40
- gi|16128030|ref|NP_414578.1| 0 0 i
41
- gi|49175993|ref|NP_414579.3| 0 0 i
42
- gi|16128032|ref|NP_414580.1| 0 0 i
43
- gi|16128033|ref|NP_414581.1| 0 0 i
44
- gi|16128034|ref|NP_414582.1| 12 0 i12-30o50-71i91-116o145-163i195-216o228-251i263-286o318-335i347-366o406-425i446-466o472-495i
45
- gi|90111081|ref|NP_414583.2| 0 0 i
46
- gi|16128036|ref|NP_414584.1| 0 0 i
47
- gi|16128037|ref|NP_414585.1| 0 Y n8-19c25/26o
48
- gi|16128038|ref|NP_414586.1| 0 0 i
49
- gi|16128039|ref|NP_414587.1| 12 0 i20-42o54-74i86-104o110-132i144-166o172-193i242-263o283-303i310-329o335-358i370-390o402-421i
50
- gi|16128040|ref|NP_414588.1| 0 0 i
51
- gi|16128041|ref|NP_414589.1| 13 0 o6-24i31-49o55-72i84-111o117-135i147-169o181-202i214-233o239-258i270-290o296-315i327-348o360-378i
52
- gi|16128042|ref|NP_414590.1| 0 Y n2-10c15/16o
53
- gi|16128043|ref|NP_414591.1| 0 0 i
data/test_files/s01_anC1_ld020mM.key.txt DELETED
@@ -1,25 +0,0 @@
1
-
2
- This is a method file from /project/marcotte/marcotte/ms/john/methods/mudpit-0.1
3
-
4
- The MS Pump gradient is this:
5
-
6
- TIME A% B% C% D% ul/min
7
- 0.00 95.0 5.0 0.0 0.0 38.0
8
- 1.00 90.0 10.0 0.0 0.0 38.0
9
- 30.00 85.0 15.0 0.0 0.0 38.0
10
- 40.00 80.0 20.0 0.0 0.0 38.0
11
- 45.00 78.0 22.0 0.0 0.0 38.0
12
- 50.00 72.0 28.0 0.0 0.0 38.0
13
- 65.00 60.0 40.0 0.0 0.0 38.0
14
- 72.00 10.0 90.0 0.0 0.0 38.0
15
- 75.0 10.0 90.0 0.0 0.0 38.0
16
- 81.00 10.0 90.0 0.0 0.0 38.0
17
- 81.10 95.0 5.0 0.0 0.0 38.0
18
- 90.00 95.0 5.0 0.0 0.0 38.0
19
- # [blank 100.0 0.0 0.0 0.0 10.0] ** is this line valid?
20
-
21
- The Sample Pump gradient is this:
22
- 0.00 0.0 0.0 100.0 0.0 40.0
23
- 90.0 0.0 0.0 100.0 0.0 40.0
24
- # [blank 100.0 0.0 0.0 0.0 10.0] ** is this line valid?
25
-
data/test_files/s01_anC1_ld020mM.meth DELETED
Binary file
data/test_files/small.fasta DELETED
@@ -1,297 +0,0 @@
1
- >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12]
2
- MKRISTTITTTITITTGNGAG
3
- >gi|16127996|ref|NP_414543.1| bifunctional aspartokinase I/homeserine dehydrogenase I [Escherichia coli K12]
4
- MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERI
5
- FAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEA
6
- RGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYS
7
- AAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPC
8
- LIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLIT
9
- QSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
10
- ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSW
11
- LKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV
12
- ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELM
13
- KFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIE
14
- IEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFK
15
- VKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
16
- >gi|16127997|ref|NP_414544.1| homoserine kinase [Escherichia coli K12]
17
- MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWE
18
- RFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHY
19
- DNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGF
20
- IHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVA
21
- DWLGKNYLQNQEGFVHICRLDTAGARVLEN
22
- >gi|16127998|ref|NP_414545.1| threonine synthase [Escherichia coli K12]
23
- MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQE
24
- ILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAA
25
- VAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNS
26
- ANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVP
27
- RFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTS
28
- EPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL
29
- RKLMMNHQ
30
- >gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli K12]
31
- MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGWWKQHYEWRGNRWHL
32
- HGPPPPPRHHKKAPHDHHGGHGPGKHHR
33
- >gi|16128000|ref|NP_414547.1| hypothetical protein b0006 [Escherichia coli K12]
34
- MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINAARFHDWQPD
35
- FTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARG
36
- KDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKK
37
- ARGLMSRFIIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR
38
- >gi|16128001|ref|NP_414548.1| inner membrane transport protein [Escherichia coli K12]
39
- MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTSFQSLCTSLAA
40
- RVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMR
41
- WMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPL
42
- MAIIWVLTSLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPN
43
- AAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAE
44
- FVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMACMA
45
- ITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE
46
- >gi|16128002|ref|NP_414549.1| transaldolase [Escherichia coli K12]
47
- MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAKQQSNDRAQQI
48
- VDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGI
49
- RAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIY
50
- QYYKEHGYETVVMGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESE
51
- FLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL
52
- >gi|16128003|ref|NP_414550.1| molybdenum cofactor biosynthesis protein [Escherichia coli K12]
53
- MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELVDEMSCHLV
54
- LTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIK
55
- ETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE
56
- >gi|16128004|ref|NP_414551.1| putative regulator, integral membrane protein [Escherichia coli K12]
57
- MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNTFGLTAFT
58
- SYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGARVLQFVFFSLTVLFALLAI
59
- GNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLPIGESH
60
- >gi|16128005|ref|NP_414552.1| hypothetical protein b0011 [Escherichia coli K12]
61
- MNVNYLNDSDLDFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHRRNWQLIAGEL
62
- QHFGGDSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLHA
63
- VDARVNELEELLPLLMKDKLLAKGVSHLLSSQLTRILRTHAAMSVLGHGLLRGAGLGGPVGAALNGVKAV
64
- SGSAYRVTIPAVLQIACLRRMVSATQV
65
- >gi|90111078|ref|NP_414553.2| positive regulator for sigma 32 heat shock promoters [Escherichia coli K12]
66
- MRVSWLESKCDTPFANNLSFISSGSSSSSSFTLASTACRNSCLCSSSIFFQVLRRNCSSNCCSISNVDIS
67
- LSAFSFNRFETSSKMARYNLPCPRSLLAILSPPKCCNSPAISCQLRRCCSGCPSIDLNSSLRISTLERRV
68
- LPFSLWVSNRAKFANCSSLQC
69
- >gi|16128007|ref|NP_414554.1| hypothetical protein b0013 [Escherichia coli K12]
70
- MKSVFTISASLAISLMLCCTAQANDHKLLGAIAMPRNETNDLALKLPVCRIVKRIQLSADHGDLQLSGAS
71
- VYFKAARSASQSLNIPSEIKEGQTTDWININSDNDNKRCVSKITFSGHTVNSSDMATLKIIGDD
72
- >gi|16128008|ref|NP_414555.1| molecular chaperone DnaK [Escherichia coli K12]
73
- MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIK
74
- RLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVI
75
- TVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEV
76
- DGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTD
77
- VNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQ
78
- KKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPT
79
- KHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKD
80
- KNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPAD
81
- DKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAE
82
- FEEVKDKK
83
- >gi|16128009|ref|NP_414556.1| chaperone with DnaK; heat shock protein [Escherichia coli K12]
84
- MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYG
85
- HAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPT
86
- LEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSK
87
- TLSVKIPAGVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEI
88
- EVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGG
89
- PTGEHNSPRSKSFFDGVKKFFDDLTR
90
- >gi|16128010|ref|NP_414557.1| IS186 hypothetical protein [Escherichia coli K12]
91
- MNYSHDNWSAILAHIGKPEELDTSARNAGALTRRREIRDAATLLRLGLAYGPGGMSLREVTAWAQLHDVA
92
- TLSDVALLKRLRNAADWFGILAAQTLAVRAAVTGCTSGKRLRLVDGTAISAPGGGSAEWRLHMGYDPHTC
93
- QFTDFELTDSRDAERLDRFAQTADEIRIADRGFGSRPECIRSLAFGEADYIVRVHWRGLRWLTAEGMRFD
94
- MMGFLRGLDCGKNGETTVMIGNSGNKKAGAPFPARLIAVSLPPEKALISKTRLLSENRRKGRVVQAETLE
95
- AAGHVLLLTSLPEDEYSAEQVADCYRLRWQIELAFKRLKSLLHLDALRAKEPELAKAWIFANLLAAFLID
96
- DIIQPSLDFPPRSAGSEKKN
97
- >gi|16128011|ref|NP_414558.1| IS186 and IS421 hypothetical protein [Escherichia coli K12]
98
- MPERELRLFYYLNCLSLQWFHRSYRNPARAENPSCQSAFLLQLTSAILASEPGRYNQLLQKQVSGYIRDA
99
- NRIPGQQCVSRLPFAQIGPAVQRLCCRLAQNQ
100
- >gi|16128012|ref|NP_414559.1| regulatory peptide whose translation enables hokC (gef) expression [Escherichia coli K12]
101
- MLNTCRVPLTDRKVKEKRAMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
102
- >gi|49175991|ref|YP_025292.1| small toxic membrane polypeptide [Escherichia coli K12]
103
- MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
104
- >gi|16128013|ref|NP_414560.1| Na+/H antiporter, pH dependent [Escherichia coli K12]
105
- MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNMLLWINDALMAV
106
- FFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYADPITREGWAIPAATDIAFALGV
107
- LALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLSMASLGVAAVAIAVLAVLNLCGARRTGVYIL
108
- VGVVLWTAVLKSGVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVT
109
- LDGLTSILPLGIIAGLLIGKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAF
110
- GSVDPELINWAKLGILVGSISSAVIGYSWLRVRLRPSV
111
- >gi|16128014|ref|NP_414561.1| transcriptional activator of cation transport (LysR family) [Escherichia coli K12]
112
- MSMSHINYNHLYYFWHVYKEGSVVGAAEALYLTPQTITGQIRALEERLQGKLFKRKGRGLEPSELGELVY
113
- RYADKMFTLSQEMLDIVNYRKESNLLFDVGVADALSKRLVSSVLNAAVVEGEPIHLRCFESTHEMLLEQL
114
- SQHKLDMIISDCPIDSTQQEGLFSVRIGECGVSFWCTNPPPEKPFPACLEERRLLIPGRRSMLGRKLLNW
115
- FNSQGLNVEILGEFDDAALMKAFGAMHNAIFVAPTLYAYDFYADKTVVEIGRVENVMEEYHAIFAERMIQ
116
- HPAVQRICNTDYSALFSPAVR
117
- >gi|16128015|ref|NP_414562.1| IS1 protein InsB [Escherichia coli K12]
118
- MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLFYAYDSLRKTV
119
- VAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLG
120
- RKSLSFSKSVELHDKVIGHYLNIKHYQ
121
- >gi|16128016|ref|NP_414563.1| IS1 protein InsA [Escherichia coli K12]
122
- MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTYTASQPGTHQKIIDMAMNGVGCRATA
123
- RIMGVGLNTILRHLKNSGRSR
124
- >gi|16128017|ref|NP_414564.1| 30S ribosomal protein S20 [Escherichia coli K12]
125
- MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKN
126
- KAARHKANLTAQINKLA
127
- >gi|16128018|ref|NP_414565.1| unknown CDS [Escherichia coli K12]
128
- MCRHSLRSDGAGFYQLAGCEYSFSAIKIAAGGQFLPVICAMAMKSHFFLISVLNRRLTLTAVQGILGRFS
129
- LF
130
- >gi|16128019|ref|NP_414566.1| hypothetical protein b0025 [Escherichia coli K12]
131
- MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGRKRNLPVMVMLFEPQPLELFATDKAPA
132
- RLTRLREKLRYLAECGVDYVLCVRFDRRFAALTAQNFISDLLVKHLRVKFLAVGDDFRFGAGREGDFLLL
133
- QKAGMEYGFDITSTQTFCEGGVRISSTAVRQALADDNLALAESLLGHPFAISGRVVHGDELGRTIGFPTA
134
- NVPLRRQVSPVKGVYAVEVLGLGEKPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLRKKI
135
- RNEQRFASLDELKAQIARDELTAREFFGLTKPA
136
- >gi|16128020|ref|NP_414567.1| isoleucyl-tRNA synthetase [Escherichia coli K12]
137
- MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSV
138
- NKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKD
139
- FIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSI
140
- DVAFQAVDQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVES
141
- VMQRIGVTDYTILGTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYG
142
- LETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWRHKTPIIFRATPQ
143
- WFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTL
144
- ELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYL
145
- EGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVA
146
- STDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAKAAQEDIL
147
- KAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQTALYHIAEALVRWMAPILSFT
148
- ADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAV
149
- TLYAEPELSAKLTALGDELRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQD
150
- VGKVAEHAEICGRCVSNVAGDGEKRKFA
151
- >gi|16128021|ref|NP_414568.1| signal peptidase II [Escherichia coli K12]
152
- MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPSLNLHYARNYGAAFSFLADSGGWQRW
153
- FFAGIAIGISVILAVMMYRSKATQKLNNIAYALIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLA
154
- DTAICVGAALIVLEGFLPSRAKKQ
155
- >gi|16128022|ref|NP_414569.1| FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) [Escherichia coli K12]
156
- MSESVQSNSAVLVHFTLKLDDGTTAESTRNNGKPALFRLGDASLSEGLEQHLLGLKVGDKTTFSLEPDAA
157
- FGVPSPDLIQYFSRREFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEV
158
- LEIDPALEA
159
- >gi|16128023|ref|NP_414570.1| 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [Escherichia coli K12]
160
- MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILI
161
- FSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGG
162
- MYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRAL
163
- AEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVA
164
- RLQQLGGGEAIPLEGREENIVFEVPKELRVDIREVD
165
- >gi|16128024|ref|NP_414571.1| nucleoside hydrolase [Escherichia coli K12]
166
- MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNAEIPLAQGAAVPL
167
- VRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAFLAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECK
168
- PYIRRLVIMGGSAGRGNCTPNAEFNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRT
169
- GKMLHALFSHYRSGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPAN
170
- VQVALDLDVKGFQQWVAEVLALAS
171
- >gi|16128025|ref|NP_414572.1| dihydrodipicolinate reductase [Escherichia coli K12]
172
- MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVK
173
- DDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLL
174
- EKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFAT
175
- VRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL
176
- >gi|16128026|ref|NP_414573.1| carbamoyl-phosphate synthase small subunit [Escherichia coli K12]
177
- MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTNDADE
178
- ESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDNPDA
179
- ALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLV
180
- DRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASG
181
- AKTVKMKFGHHGGNHPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSF
182
- QGHPEASPGPHDAAPLFDHFIELIEQYRKTAK
183
- >gi|16128027|ref|NP_414574.1| carbamoyl-phosphate synthase large subunit [Escherichia coli K12]
184
- MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIH
185
- WEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIG
186
- LETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESL
187
- IGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETG
188
- GSNVQFAVNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEP
189
- SIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA
190
- LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLR
191
- QLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANPSTDRE
192
- KIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIV
193
- RIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM
194
- AVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDG
195
- EMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI
196
- EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPE
197
- MRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIV
198
- LGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFAT
199
- AMALNADATEKVISVQEMHAQIK
200
- >gi|90111079|ref|NP_414576.4| transcriptional regulator of cai operon [Escherichia coli K12]
201
- MCEGYVEKPLYLLIAEWMMAENRWVIAREISIHFDIEHSKAVNTLTYILSEVTEISCEVKMIPNKLEGRG
202
- CQCQRLVKVVDIDEQIYARLRNNSREKLVGVRKTPRIPAVPLTELNREQKWQMMLSKSMRR
203
- >gi|90111080|ref|NP_414577.2| possible synthesis of cofactor for carnitine racemase and dehydratase [Escherichia coli K12]
204
- MSYYAFEGLIPVVHPTAFVHPSAVLIGDVIVGAGVYIGPLASLRGDYGRLIVQAGANIQDGCIMHGYCDT
205
- DTIVGENGHIGHGAILHGCLIGRDALVGMNSVIMDGAVIGEESIVAAMSFVKAGFRGEKRQLLMGTPARA
206
- VRNVSDDELHWKRLNTKEYQDLVGRCHVSLHETQPLRQMEENRPRLQGTTDVTPKR
207
- >gi|16128030|ref|NP_414578.1| carnitinyl-CoA dehydratase [Escherichia coli K12]
208
- MKQQGTTLPANNHTLKQYAFFAGMLSSLKKQKWRKGMSESLHLTRNGSILEITLDRPKANAIDAKTSFEM
209
- GEVFLNFRDDPQLRVAIITGAGEKFFSAGWDLKAAAEGEAPDADFGPGGFAGLTEIFNLDKPVIAAVNGY
210
- AFGGGFELALAADFIVCADNASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWG
211
- IVNRVVSQAELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHSEDAI
212
- EGPLAFAEKRDPVWKGR
213
- >gi|49175993|ref|NP_414579.3| crotonobetaine/carnitine-CoA ligase [Escherichia coli K12]
214
- MDRGAMDIIGGQHLRQMWDDLADVYGHKTALICESSGGVVNRYSYLELNQEINRTANLFYTLGIRKGDKV
215
- ALHLDNCPEFIFCWFGLAKIGAIMVPINARLLCEESAWILQNSQACLLVTSAQFYPMYQQIQQEDATQLR
216
- HICLTDVALPADDGVSSFTQLKNQQPATLCYAPPLSTDDTAEILFTSGTTSRPKGVVITHYNLRFAGYYS
217
- AWQCALRDDDVYLTVMPAFHIDCQCTAAMAAFSAGATFVLVEKYSARAFWGQVQKYRATVTECIPMMIRT
218
- LMVQPPSANDQQHRLREVMFYLNLSEQEKDAFCERFGVRLLTSYGMTETIVGIIGDRPGDKRRWPSIGRV
219
- GFCYEAEIRDDHNRPLPAGEIGEICIKGIPGKTIFKEYFLNPQATAKVLEADGWLHTGDTGYRDEEDFFY
220
- FVDRRCNMIKRGGENVSCVELENIIAAHPKIQDIVVVGIKDSIRDEAIKAFVVLNEGETLSEEEFFRFCE
221
- QNMAKFKVPSYLEIRKDLPRNCSGKIIRKNLK
222
- >gi|16128032|ref|NP_414580.1| crotonobetainyl-CoA:carnitineCoA-transferase [Escherichia coli K12]
223
- MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALS
224
- LNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAY
225
- NTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQY
226
- FMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQL
227
- IHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRT
228
- CKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED
229
- >gi|16128033|ref|NP_414581.1| crotonobetainyl-CoA dehydrogenase [Escherichia coli K12]
230
- MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPEEHGGLDAGFVTL
231
- AAVWMELGRLGAPTYVLYQLPGGFNTFLREGTQEQIDKIMAFRGTGKQMWNSAITEPGAGSDVGSLKTTY
232
- TRRNGKIYLNGSKCFITSSAYTPYIVVMARDGASPDKPVYTEWFVDMSKPGIKVTKLEKLGLRMDSCCEI
233
- TFDDVELDEKDMFGREGNGFNRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQ
234
- EKFAHMAIKLNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRF
235
- WRDLRVDRVSGGSDEMQILTLGRAVLKQYR
236
- >gi|16128034|ref|NP_414582.1| L-carnitine/gamma-butyrobetaine antiporter [Escherichia coli K12]
237
- MKNEKRKTGIEPKVFFPPLIIVGILCWLTVRDLDAANVVINAVFSYVTNVWGWAFEWYMVVMLFGWFWLV
238
- FGPYAKKRLGNEPPEFSTASWIFMMFASCTSAAVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLF
239
- HWGPLPWATYSFLSVAFAYFFFVRKMEVIRPSSTLVPLVGEKHAKGLFGTIVDNFYLVALIFAMGTSLGL
240
- ATPLVTECMQWLFGIPHTLQLDAIIITCWIILNAICVACGLQKGVRIASDVRSYLSFLMLGWVFIVSGAS
241
- FIMNYFTDSVGMLLMYLPRMLFYTDPIAKGGFPQGWTVFYWAWWVIYAIQMSIFLARISRGRTVRELCFG
242
- MVLGLTASTWILWTVLGSNTLLLIDKNIINIPNLIEQYGVARAIIETWAALPLSTATMWGFFILCFIATV
243
- TLVNACSYTLAMSTCREVRDGEEPPLLVRIGWSILVGIIGIVLLALGGLKPIQTAIIAGGCPLFFVNIMV
244
- TLSFIKDAKQNWKD
245
- >gi|90111081|ref|NP_414583.2| putative electron transfer flavoprotein subunit beta [Escherichia coli K12]
246
- MKIITCYKCVPDEQDIAVNNADGSLDFSKADAKISQYDLNAIEAACQLKQQAAEAQVTALSVGGKALTNA
247
- KGRKDVLSRGPDELIVVIDDQFEQALPQQTASALAAAAQKAGFDLILCGDGSSDLYAQQVGLLVGEILNI
248
- PAVNGVSKIISLTADTLTVERELEDETETLSIPLPAVVAVSTDINSPQIPSMKAILGAAKKPVQVWSAAD
249
- IGFNAEAAWSEQQVAAPKQRERQRIVIEGDGEEQIAAFAENLRKVI
250
- >gi|16128036|ref|NP_414584.1| putative electron transfer flavoprotein subunit alpha [Escherichia coli K12]
251
- MNTFSQVWVFSDTPSRLPELMNGAQALANQINTFVLNDADGAQAIQLGANHVWKLNGKPDDRMIEDYAGV
252
- MADTIRQHGADGLVLLPNTRRGKLLAAKLGYRLKAAVSNDASTVSVQDGKATVKHMVYGGLAIGEERIAT
253
- PYAVLTISSGTFDAAQPDASRTGETHTVEWQAPAVAITRTATQARQSNSVDLDKARLVVSVGRGIGSKEN
254
- IALAEQLCKAIGAELACSRPVAENEKWMEHERYVGISNLMLKPELYLAVGISGQIQHMVGANASQTIFAI
255
- NKDKNAPIFQYADYGIVGDAVKILPALTAALAR
256
- >gi|16128037|ref|NP_414585.1| carnitine metabolism related [Escherichia coli K12]
257
- MSEDIFDAIIVGAGLAGSVAALVLAREGAQVLVIERGNSAGAKNVTGGRLYAHSLEHIIPGFADSAPVER
258
- LITHEKLAFMTEKSAMTMDYCNGDETSPSQRSYSVLRSKFDAWLMEQAEEAGAQLITGIRVDNLVQRDGK
259
- VVGVEADGDVIEAKTVILADGVNSILAEKLGMAKRVKPTDVAVGVKELIELPKSVIEDRFQLQGNQGAAC
260
- LFAGSPTDGLMGGGFLYTNENTLSLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEYSAHV
261
- VPEAGINMLPELVGDGVLIAGDAAGMCMNLGFTIRGMDLAIAAGEAAAKTVLSAMKSDDFSKQKLAEYRQ
262
- HLESGPLRDMRMYQKLPAFLDNPRMFSGYPELAVGVARDLFTIDGSAPELMRKKILRHGKKVGFINLIKD
263
- GMKGVTVL
264
- >gi|16128038|ref|NP_414586.1| putative ferredoxin [Escherichia coli K12]
265
- MTSPVNVDVKLGVNKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDDGSVRFDYAGCLECGTCR
266
- ILGLGSALEQWEYPRGTFGVEFRYG
267
- >gi|16128039|ref|NP_414587.1| putative transport protein [Escherichia coli K12]
268
- MQPSRNFDDLKFSSIHRRILLWGSGGPFLDGYVLVMIGVALEQLTPALKLDADWIGLLGAGTLAGLFVGT
269
- SLFGYISDKVGRRKMFLIDIIAIGVISVATMFVSSPVELLVMRVLIGIVIGADYPIATSMITEFSSTRQR
270
- AFSISFIAAMWYVGATCADLVGYWLYDVEGGWRWMLGSAAIPCLLILIGRFELPESPRWLLRKGRVKECE
271
- EMMIKLFGEPVAFDEEQPQQTRFRDLFNRRHFPFVLFVAAIWTCQVIPMFAIYTFGPQIVGLLGLGVGKN
272
- AALGNVVISLFFMLGCIPPMLWLNTAGRRPLLIGSFAMMTLALAVLGLIPDMGIWLVVMAFAVYAFFSGG
273
- PGNLQWLYPNELFPTDIRASAVGVIMSLSRIGTIVSTWALPIFINNYGISNTMLMGAGISLFGLLISVAF
274
- APETRGMSLAQTSNMTIRGQRMG
275
- >gi|16128040|ref|NP_414588.1| glutathione-regulated potassium-efflux system ancillary protein [Escherichia coli K12]
276
- MILIIYAHPYPHHSHANKRMLEQARTLEGVEIRSLYQLYPDFNIDIAAEQEALSRADLIVWQHPMQWYSI
277
- PPLLKLWIDKVFSHGWAYGHGGTALHGKHLLWAVTTGGGESHFEIGAHPGFDVLSQPLQATAIYCGLNWL
278
- PPFAMHCTFICDDETLEGQARHYKQRLLEWQEAHHG
279
- >gi|16128041|ref|NP_414589.1| glutathione-regulated potassium-efflux system protein [Escherichia coli K12]
280
- MDSHTLIQALIYLGSAALIVPIAVRLGLGSVLGYLIAGCIIGPWGLRLVTDAESILHFAEIGVVLMLFII
281
- GLELDPQRLWKLRAAVFGCGALQMVICGGLLGLFCMLLGLRWQVAELIGMTLALSSTAIAMQAMNERNLM
282
- VTQMGRSAFAVLLFQDIAAIPLVAMIPLLATSSASTTMGAFALSALKVAGALVLVVLLGRYVTRPALRFV
283
- ARSGLREVFSAVALFLVFGFGLLLEEVGLSMAMGAFLAGVLLASSEYRHALESDIEPFKGLLLGLFFIGV
284
- GMSIDFGTLLENPLRIVILLLGFLIIKIAMLWLIARPLQVPNKQRRWFAVLLGQGSEFAFVVFGAAQMAN
285
- VLEPEWAKSLTLAVALSMAATPILLVILNRLEQSSTEEAREADEIDEEQPRVIIAGFGRFGQITGRLLLS
286
- SGVKMVVLDHDPDHIETLRKFGMKVFYGDATRMDLLESAGAAKAEVLINAIDDPQTNLQLTEMVKEHFPH
287
- LQIIARARDVDHYIRLRQAGVEKPERETFEGALKTGRLALESLGLGPYEARERADVFRRFNIQMVEEMAM
288
- VENDTKARAAVYKRTSAMLSEIITEDREHLSLIQRHGWQGTEEGKHTGNMADEPETKPSS
289
- >gi|16128042|ref|NP_414590.1| dihydrofolate reductase type I, trimethoprim resistance [Escherichia coli K12]
290
- MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDD
291
- RVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEF
292
- HDADAQNSHSYCFEILERR
293
- >gi|16128043|ref|NP_414591.1| diadenosinetetraphosphatase [Escherichia coli K12]
294
- MATYLIGDVHGCYDELIALLHKVEFTPGKDTLWLTGDLVARGPGSLDVLRYVKSLGDSVRLVLGNHDLHL
295
- LAVFAGISRNKPKDRLTPLLEAPDADELLNWLRRQPLLQIDEEKKLVMAHAGITPQWDLQTAKECARDVE
296
- AVLSSDSYPFFLDAMYGDMPNNWSPELRGLGRLRFITNAFTRMRFCFPNGQLDMYSKESPEEAPAPLKPW
297
- FAIPGPVAEEYSIAFGHWASLEGKGTPEGIYALDTGCCWGGTLTCLRWEDKQYFVQPSNRHKDLGEAAAS
data/test_files/small.sqt DELETED
@@ -1,87 +0,0 @@
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|
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/test_files/smallraw.RAW DELETED
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