mspire 0.2.4 → 0.3.0

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Files changed (233) hide show
  1. data/INSTALL +1 -0
  2. data/README +25 -0
  3. data/Rakefile +129 -40
  4. data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
  5. data/bin/bioworks_to_pepxml.rb +1 -0
  6. data/bin/fasta_shaker.rb +1 -96
  7. data/bin/filter_and_validate.rb +5 -0
  8. data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
  9. data/bin/prob_validate.rb +6 -0
  10. data/bin/raw_to_mzXML.rb +2 -2
  11. data/bin/srf_group.rb +1 -0
  12. data/bin/srf_to_sqt.rb +40 -0
  13. data/changelog.txt +68 -0
  14. data/lib/align/chams.rb +6 -6
  15. data/lib/align.rb +4 -3
  16. data/lib/bsearch.rb +120 -0
  17. data/lib/fasta.rb +318 -86
  18. data/lib/group_by.rb +10 -0
  19. data/lib/index_by.rb +11 -0
  20. data/lib/merge_deep.rb +21 -0
  21. data/lib/{spec → ms/converter}/mzxml.rb +77 -109
  22. data/lib/ms/gradient_program.rb +171 -0
  23. data/lib/ms/msrun.rb +209 -0
  24. data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
  25. data/lib/ms/parser/mzdata/axml.rb +12 -0
  26. data/lib/ms/parser/mzdata/dom.rb +160 -0
  27. data/lib/ms/parser/mzdata/libxml.rb +7 -0
  28. data/lib/ms/parser/mzdata.rb +25 -0
  29. data/lib/ms/parser/mzxml/axml.rb +11 -0
  30. data/lib/ms/parser/mzxml/dom.rb +159 -0
  31. data/lib/ms/parser/mzxml/hpricot.rb +253 -0
  32. data/lib/ms/parser/mzxml/libxml.rb +15 -0
  33. data/lib/ms/parser/mzxml/regexp.rb +122 -0
  34. data/lib/ms/parser/mzxml/rexml.rb +72 -0
  35. data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
  36. data/lib/ms/parser/mzxml.rb +175 -0
  37. data/lib/ms/parser.rb +108 -0
  38. data/lib/ms/precursor.rb +10 -0
  39. data/lib/ms/scan.rb +81 -0
  40. data/lib/ms/spectrum.rb +193 -0
  41. data/lib/ms.rb +10 -0
  42. data/lib/mspire.rb +4 -0
  43. data/lib/roc.rb +61 -1
  44. data/lib/sample_enzyme.rb +31 -8
  45. data/lib/scan_i.rb +21 -0
  46. data/lib/spec_id/aa_freqs.rb +7 -3
  47. data/lib/spec_id/bioworks.rb +20 -14
  48. data/lib/spec_id/digestor.rb +139 -0
  49. data/lib/spec_id/mass.rb +116 -0
  50. data/lib/spec_id/parser/proph.rb +236 -0
  51. data/lib/spec_id/precision/filter/cmdline.rb +209 -0
  52. data/lib/spec_id/precision/filter/interactive.rb +134 -0
  53. data/lib/spec_id/precision/filter/output.rb +147 -0
  54. data/lib/spec_id/precision/filter.rb +623 -0
  55. data/lib/spec_id/precision/output.rb +60 -0
  56. data/lib/spec_id/precision/prob/cmdline.rb +139 -0
  57. data/lib/spec_id/precision/prob/output.rb +88 -0
  58. data/lib/spec_id/precision/prob.rb +171 -0
  59. data/lib/spec_id/proph/pep_summary.rb +92 -0
  60. data/lib/spec_id/proph/prot_summary.rb +484 -0
  61. data/lib/spec_id/proph.rb +2 -466
  62. data/lib/spec_id/protein_summary.rb +2 -2
  63. data/lib/spec_id/sequest/params.rb +316 -0
  64. data/lib/spec_id/sequest/pepxml.rb +1513 -0
  65. data/lib/spec_id/sequest.rb +2 -1672
  66. data/lib/spec_id/srf.rb +445 -177
  67. data/lib/spec_id.rb +183 -95
  68. data/lib/spec_id_xml.rb +8 -10
  69. data/lib/transmem/phobius.rb +147 -0
  70. data/lib/transmem/toppred.rb +368 -0
  71. data/lib/transmem.rb +157 -0
  72. data/lib/validator/aa.rb +135 -0
  73. data/lib/validator/background.rb +73 -0
  74. data/lib/validator/bias.rb +95 -0
  75. data/lib/validator/cmdline.rb +260 -0
  76. data/lib/validator/decoy.rb +94 -0
  77. data/lib/validator/digestion_based.rb +69 -0
  78. data/lib/validator/probability.rb +48 -0
  79. data/lib/validator/prot_from_pep.rb +234 -0
  80. data/lib/validator/transmem.rb +272 -0
  81. data/lib/validator/true_pos.rb +46 -0
  82. data/lib/validator.rb +214 -0
  83. data/lib/xml.rb +38 -0
  84. data/lib/xml_style_parser.rb +105 -0
  85. data/lib/xmlparser_wrapper.rb +19 -0
  86. data/script/compile_and_plot_smriti_final.rb +97 -0
  87. data/script/extract_gradient_programs.rb +56 -0
  88. data/script/get_apex_values_rexml.rb +44 -0
  89. data/script/mzXML2timeIndex.rb +1 -1
  90. data/script/smriti_final_analysis.rb +103 -0
  91. data/script/toppred_to_yaml.rb +47 -0
  92. data/script/tpp_installer.rb +1 -1
  93. data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
  94. data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
  95. data/specs/bin/fasta_shaker_spec.rb +259 -0
  96. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
  97. data/specs/bin/filter_and_validate_spec.rb +124 -0
  98. data/specs/bin/ms_to_lmat_spec.rb +34 -0
  99. data/specs/bin/prob_validate_spec.rb +62 -0
  100. data/specs/bin/protein_summary_spec.rb +10 -0
  101. data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
  102. data/specs/gi_spec.rb +22 -0
  103. data/specs/load_bin_path.rb +7 -0
  104. data/specs/merge_deep_spec.rb +13 -0
  105. data/specs/ms/gradient_program_spec.rb +77 -0
  106. data/specs/ms/msrun_spec.rb +455 -0
  107. data/specs/ms/parser_spec.rb +92 -0
  108. data/specs/ms/spectrum_spec.rb +89 -0
  109. data/specs/roc_spec.rb +251 -0
  110. data/specs/rspec_autotest.rb +149 -0
  111. data/specs/sample_enzyme_spec.rb +41 -0
  112. data/specs/spec_helper.rb +133 -0
  113. data/specs/spec_id/aa_freqs_spec.rb +52 -0
  114. data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
  115. data/specs/spec_id/digestor_spec.rb +75 -0
  116. data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
  117. data/specs/spec_id/precision/filter/output_spec.rb +31 -0
  118. data/specs/spec_id/precision/filter_spec.rb +243 -0
  119. data/specs/spec_id/precision/prob_spec.rb +111 -0
  120. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  121. data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
  122. data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
  123. data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
  124. data/specs/spec_id/sequest/params_spec.rb +68 -0
  125. data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
  126. data/specs/spec_id/sqt_spec.rb +138 -0
  127. data/specs/spec_id/srf_spec.rb +209 -0
  128. data/specs/spec_id/srf_spec_helper.rb +302 -0
  129. data/specs/spec_id_helper.rb +33 -0
  130. data/specs/spec_id_spec.rb +361 -0
  131. data/specs/spec_id_xml_spec.rb +33 -0
  132. data/specs/transmem/phobius_spec.rb +423 -0
  133. data/specs/transmem/toppred_spec.rb +297 -0
  134. data/specs/transmem_spec.rb +60 -0
  135. data/specs/transmem_spec_shared.rb +64 -0
  136. data/specs/validator/aa_spec.rb +107 -0
  137. data/specs/validator/background_spec.rb +51 -0
  138. data/specs/validator/bias_spec.rb +146 -0
  139. data/specs/validator/decoy_spec.rb +51 -0
  140. data/specs/validator/fasta_helper.rb +26 -0
  141. data/specs/validator/prot_from_pep_spec.rb +141 -0
  142. data/specs/validator/transmem_spec.rb +145 -0
  143. data/specs/validator/true_pos_spec.rb +58 -0
  144. data/specs/validator_helper.rb +33 -0
  145. data/specs/xml_spec.rb +12 -0
  146. data/test_files/000_pepxml18_small.xml +206 -0
  147. data/test_files/020a.mzXML.timeIndex +4710 -0
  148. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
  149. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
  150. data/test_files/4-03-03_small-prot.xml +321 -0
  151. data/test_files/4-03-03_small.xml +3876 -0
  152. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  153. data/test_files/bioworks-3.3_10prots.xml +5999 -0
  154. data/test_files/bioworks31.params +77 -0
  155. data/test_files/bioworks32.params +62 -0
  156. data/test_files/bioworks33.params +63 -0
  157. data/test_files/bioworks_single_run_small.xml +7237 -0
  158. data/test_files/bioworks_small.fasta +212 -0
  159. data/test_files/bioworks_small.params +63 -0
  160. data/test_files/bioworks_small.phobius +109 -0
  161. data/test_files/bioworks_small.toppred.out +2847 -0
  162. data/test_files/bioworks_small.xml +5610 -0
  163. data/test_files/bioworks_with_INV_small.xml +3753 -0
  164. data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
  165. data/test_files/corrupted_900.srf +0 -0
  166. data/test_files/head_of_7MIX.srf +0 -0
  167. data/test_files/interact-opd1_mods_small-prot.xml +304 -0
  168. data/test_files/messups.fasta +297 -0
  169. data/test_files/opd1/000.my_answer.100lines.xml +101 -0
  170. data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
  171. data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
  172. data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
  173. data/test_files/opd1/000_020-prot.png +0 -0
  174. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
  175. data/test_files/opd1/000_020_3prots-prot.xml +62 -0
  176. data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
  177. data/test_files/opd1/sequest.3.1.params +77 -0
  178. data/test_files/opd1/sequest.3.2.params +62 -0
  179. data/test_files/opd1/twenty_scans.mzXML +418 -0
  180. data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
  181. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  182. data/test_files/opd1/twenty_scans_answ.lmata +9 -0
  183. data/test_files/opd1_020_beginning.RAW +0 -0
  184. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
  185. data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
  186. data/test_files/pepproph_small.xml +4691 -0
  187. data/test_files/phobius.small.noheader.txt +50 -0
  188. data/test_files/phobius.small.small.txt +53 -0
  189. data/test_files/s01_anC1_ld020mM.key.txt +25 -0
  190. data/test_files/s01_anC1_ld020mM.meth +0 -0
  191. data/test_files/small.fasta +297 -0
  192. data/test_files/smallraw.RAW +0 -0
  193. data/test_files/tf_bioworks2excel.bioXML +14340 -0
  194. data/test_files/tf_bioworks2excel.txt.actual +1035 -0
  195. data/test_files/toppred.small.out +416 -0
  196. data/test_files/toppred.xml.out +318 -0
  197. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
  198. data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
  199. data/test_files/yeast_gly_small-prot.xml +265 -0
  200. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
  201. data/test_files/yeast_gly_small.xml +3807 -0
  202. data/test_files/yeast_gly_small2.parentTimes +6 -0
  203. metadata +273 -57
  204. data/bin/filter.rb +0 -6
  205. data/bin/precision.rb +0 -5
  206. data/lib/spec/mzdata/parser.rb +0 -108
  207. data/lib/spec/mzdata.rb +0 -48
  208. data/lib/spec/mzxml/parser.rb +0 -449
  209. data/lib/spec/scan.rb +0 -55
  210. data/lib/spec_id/filter.rb +0 -797
  211. data/lib/spec_id/precision.rb +0 -421
  212. data/lib/toppred.rb +0 -18
  213. data/script/filter-peps.rb +0 -164
  214. data/test/tc_aa_freqs.rb +0 -59
  215. data/test/tc_fasta_shaker.rb +0 -149
  216. data/test/tc_filter.rb +0 -203
  217. data/test/tc_filter_peps.rb +0 -46
  218. data/test/tc_gi.rb +0 -17
  219. data/test/tc_id_class_anal.rb +0 -70
  220. data/test/tc_id_precision.rb +0 -89
  221. data/test/tc_msrun.rb +0 -88
  222. data/test/tc_mzxml.rb +0 -88
  223. data/test/tc_mzxml_to_lmat.rb +0 -36
  224. data/test/tc_peptide_parent_times.rb +0 -27
  225. data/test/tc_precision.rb +0 -60
  226. data/test/tc_roc.rb +0 -166
  227. data/test/tc_sample_enzyme.rb +0 -32
  228. data/test/tc_scan.rb +0 -26
  229. data/test/tc_sequest.rb +0 -336
  230. data/test/tc_spec.rb +0 -78
  231. data/test/tc_spec_id.rb +0 -201
  232. data/test/tc_spec_id_xml.rb +0 -36
  233. data/test/tc_srf.rb +0 -262
data/test_files/phobius.small.noheader.txt ADDED
@@ -0,0 +1,50 @@
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 ADDED
@@ -0,0 +1,53 @@
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 ADDED
@@ -0,0 +1,25 @@
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 ADDED
Binary file
data/test_files/small.fasta ADDED
@@ -0,0 +1,297 @@
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/smallraw.RAW ADDED
Binary file