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/toppred.xml.out DELETED
@@ -1,318 +0,0 @@
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- <?xml version="1.0" encoding="ISO-8859-1" ?>
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- <!DOCTYPE toppred SYSTEM "toppred.dtd">
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-
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- <toppreds>
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-
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- <parameters>
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- <corewindow>11</corewindow>
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- <wedgewindow>5</wedgewindow>
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- <certain>1.00</certain>
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- <putative>0.60</putative>
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- <distsegments>2</distsegments>
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- <looplength>60</looplength>
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- <kingdom>procaryote</kingdom>
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- <hydrophobycity>GES-scale</hydrophobycity>
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- </parameters>
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-
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- <toppred>
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- <sequence id="SWN_PWP1_HUMAN" size="501">
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- MNRSRQVTCVAWVRCGVAKETPDKVELSKEEVKRLIAEAKEKLQEEGGGSDEEETGSPSE
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- DGMQSARTQARPREPLEDGDPEDDRTLDDDELAEYDLDKYDEEGDPDAETLGESLLGLTV
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- YGSNDQDPYVTLKDTEQYEREDFLIKPSDNLIVCGRAEQDQCNLEVHVYNQEEDSFYVHH
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- DILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWDLDIVDSLEPVFTLGSKLSK
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- KKKKKGKKSSSAEGHTDAVLDLSWNKLIRNVLASASADNTVILWDMSLGKPAASLAVHTD
24
- KVQTLQFHPFEAQTLISGSYDKSVALYDCRSPDESHRMWRFSGQIERVTWNHFSPCHFLA
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- STDDGFVYNLDARSDKPIFTLNAHNDEISGLDLSSQIKGCLVTASADKYVKIWDILGDRP
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- SLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGLRVWDISTVSSVNEAFGRRERLVLGS
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- ARNSSISGPFGSRSSDTPMES
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- </sequence>
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-
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- <plot hydro="SWN_PWP1_HUMAN.hydro" gplot="SWN_PWP1_HUMAN.png"/>
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-
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- <tmsummary segments="1" len="21">
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- <segment start="430" stop="450" hp="1.074" type="certain"/>
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- </tmsummary>
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-
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- <topologies maxtopo="1" topoprint="1">
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-
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- <topology nr="1" prob="1.00" darglys="-7.00" dcytext="0.12" dncharge="1.00" dnnegpos="0.30" orient="N-out N-out N-in">
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- <loop type="unknown" start="1" stop="429" darglys="45.00" dcytext="0.12" decisive="dcytext"/>
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- <tmsegment start="430" stop="450" prob="21.00" hp="1.07"/>
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- <loop type="unknown" start="451" stop="501" darglys="7.00" dcytext="0.80" decisive="darglys"/>
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- </topology>
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-
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- </topologies>
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- </toppred>
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-
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- <toppred>
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- <sequence id="SWN_K1CL_HUMAN" size="494">
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- MDLSNNTMSLSVRTPGLSRRLSSQSVIGRPRGMSASSVGSGYGGSAFGFGASCGGGFSAA
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- SMFGSSSGFGGGSGSSMAGGLGAGYGRALGGGSFGGLGMGFGGSPGGGSLGILSGNDGGL
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- LSGSEKETMQNLNDRLASYLDKVRALEEANTELENKIREWYETRGTGTADASQSDYSKYY
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- PLIEDLRNKIISASIGNAQLLLQIDNARLAAEDFRMKYENELALRQGVEADINGLRRVLD
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- ELTLTRTDLEMQIESLNEELAYMKKNHEDELQSFRVGGPGEVSVEMDAAPGVDLTRLLND
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- MRAQYETIAEQNRKDAEAWFIEKSGELRKEISTNTEQLQSSKSEVTDLRRAFQNLEIELQ
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- SQLAMKKSLEDSLAEAEGDYCAQLSQVQQLISNLEAQLLQVRADAERQNVDHQRLLNVKA
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- RLELEIETYRRLLDGEAQGDGLEESLFVTDSKSQAQSTDSSKDPTKTRKIKTVVQEMVNG
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- EVVSSQVQEIEELM
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- </sequence>
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-
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- <plot hydro="SWN_K1CL_HUMAN.hydro" gplot="SWN_K1CL_HUMAN.png"/>
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-
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- <tmsummary segments="2" len="21">
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- <segment start="44" stop="64" hp="1.694" type="certain"/>
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- <segment start="88" stop="108" hp="1.548" type="certain"/>
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- </tmsummary>
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-
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- <topologies maxtopo="1" topoprint="1">
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-
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- <topology nr="1" prob="1.00" darglys="5.00" dcytext="-0.73" dncharge="2.00" dnnegpos="-0.67" orient="N-in N-in N-in">
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- <loop type="unknown" start="1" stop="43" darglys="5.00" dcytext="0.96" decisive="darglys"/>
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- <tmsegment start="44" stop="64" prob="21.00" hp="1.69"/>
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- <loop type="unknown" start="65" stop="87" darglys="1.00" dcytext="0.87" decisive="darglys"/>
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- <tmsegment start="88" stop="108" prob="21.00" hp="1.55"/>
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- <loop type="unknown" start="109" stop="494" darglys="45.00" dcytext="-0.73" decisive="dcytext"/>
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- </topology>
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-
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- </topologies>
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- </toppred>
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-
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- <toppred>
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- <sequence id="SWN_UBCC_HUMAN" size="152">
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- MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
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- EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
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- LANDVAEQWKTNEAQAIETARAWTRLYAMNNI
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- </sequence>
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-
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- <plot hydro="SWN_UBCC_HUMAN.hydro" gplot="SWN_UBCC_HUMAN.png"/>
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-
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- <tmsummary segments="0">
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- </tmsummary>
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- </toppred>
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-
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- <toppred>
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- <sequence id="SWN_UBCE_HUMAN" size="225">
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- MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLF
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- RMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLL
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- IHPNPESALNEEAGRLLLENYEEYAARARLLTEIHGGAGGPSGRAEAGRALASGTEASST
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- DPGAPGGPGGAEGPMAKKHAGERDKKLAAKKKTDKKRALRALRRL
99
- </sequence>
100
-
101
- <plot hydro="SWN_UBCE_HUMAN.hydro" gplot="SWN_UBCE_HUMAN.png"/>
102
-
103
- <tmsummary segments="0">
104
- </tmsummary>
105
- </toppred>
106
-
107
- <toppred>
108
- <sequence id="SWN_UFD1_HUMAN" size="343">
109
- MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAWPNDRSDVEKGGKIIMPPSALDQLSRLN
110
- ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEDGLVQLETVNLQVA
111
- TYSKSKFCYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSADFLDITNPKAVLEN
112
- ALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIHECDMNVDFDAPLGYKEPERQV
113
- QHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFK
114
- LGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSLRKKGRKP
115
- </sequence>
116
-
117
- <plot hydro="SWN_UFD1_HUMAN.hydro" gplot="SWN_UFD1_HUMAN.png"/>
118
-
119
- <tmsummary segments="0">
120
- </tmsummary>
121
- </toppred>
122
-
123
- <toppred>
124
- <sequence id="SWN_SM31_HUMAN" size="103">
125
- MSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTSLSKLMKAYCERQGLSMRQIRFR
126
- FDGQPINETDTPAQLRMEDEDTIDVFQQQTGGVPESSLAGHSF
127
- </sequence>
128
-
129
- <plot hydro="SWN_SM31_HUMAN.hydro" gplot="SWN_SM31_HUMAN.png"/>
130
-
131
- <tmsummary segments="0">
132
- </tmsummary>
133
- </toppred>
134
-
135
- <toppred>
136
- <sequence id="SWN_SM32_HUMAN" size="95">
137
- MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRF
138
- RFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVY
139
- </sequence>
140
-
141
- <plot hydro="SWN_SM32_HUMAN.hydro" gplot="SWN_SM32_HUMAN.png"/>
142
-
143
- <tmsummary segments="0">
144
- </tmsummary>
145
- </toppred>
146
-
147
- <toppred>
148
- <sequence id="SWN_SM33_HUMAN" size="101">
149
- MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN
150
- SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV
151
- </sequence>
152
-
153
- <plot hydro="SWN_SM33_HUMAN.hydro" gplot="SWN_SM33_HUMAN.png"/>
154
-
155
- <tmsummary segments="0">
156
- </tmsummary>
157
- </toppred>
158
-
159
- <toppred>
160
- <sequence id="SWN_UBPN_HUMAN" size="854">
161
- MYNVGEHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLLNWYGCVEGQQ
162
- PIVRKVVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFNI
163
- PAERETRLWNKYMSNTYEQLSKLDNTVQDAGLYQGQVLVIEPQNEDGTWPRQTLQSKSST
164
- APSRNFTTSPKSSASPYSSVSASLIANGDSTSTCGMHSSGVSRGGSGFSASYNCQEPPSS
165
- HIQPGLCGLGNLGNTCFMNSALQCLSNTHPLTDYFLKDEYEAEINRDNPLGMKGEIAEAY
166
- AELIKQMWSGRDAHVAPWMFKTQVGRFAPQFSGYQQQDSQELLAFPSRWIHEDLNRVKKK
167
- PYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFC
168
- YLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVV
169
- ADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTS
170
- SASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNS
171
- CEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSY
172
- GTADINSLAADGKLLKLNSRSTLAMDWDRETRRLYYDEQESEAYEKHVSMLQPQKKKKTT
173
- VALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWR
174
- DKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWY
175
- YFDDSNVSWPLRIR
176
- </sequence>
177
-
178
- <plot hydro="SWN_UBPN_HUMAN.hydro" gplot="SWN_UBPN_HUMAN.png"/>
179
-
180
- <tmsummary segments="3" len="21">
181
- <segment start="242" stop="262" hp="0.680" type="putative"/>
182
- <segment start="409" stop="429" hp="0.604" type="putative"/>
183
- <segment start="536" stop="556" hp="0.817" type="putative"/>
184
- </tmsummary>
185
-
186
- <topologies maxtopo="8" topoprint="7">
187
-
188
- <topology nr="1" prob="0.54" darglys="0.00" dcytext="0.78" dncharge="2.00" dnnegpos="0.12" orient="? N-out N-in">
189
- <loop type="unknown" start="1" stop="535" darglys="52.00" dcytext="0.94" decisive="dcytext"/>
190
- <tmsegment start="536" stop="556" prob="21.00" hp="0.82"/>
191
- <loop type="unknown" start="557" stop="854" darglys="41.00" dcytext="0.16" decisive="dcytext"/>
192
- </topology>
193
-
194
- <topology nr="2" prob="0.20" darglys="0.00" dcytext="0.58" dncharge="0.00" dnnegpos="0.17" orient="? N-out ?">
195
- <loop type="unknown" start="1" stop="241" darglys="20.00" dcytext="1.10" decisive="dcytext"/>
196
- <tmsegment start="242" stop="262" prob="21.00" hp="0.68"/>
197
- <loop type="unknown" start="263" stop="854" darglys="73.00" dcytext="0.52" decisive="dcytext"/>
198
- </topology>
199
-
200
- <topology nr="3" prob="0.20" darglys="0.00" dcytext="0.70" dncharge="0.00" dnnegpos="0.17" orient="? N-out ?">
201
- <loop type="unknown" start="1" stop="241" darglys="20.00" dcytext="1.10" decisive="dcytext"/>
202
- <tmsegment start="242" stop="262" prob="21.00" hp="0.68"/>
203
- <loop type="unknown" start="263" stop="535" darglys="32.00" dcytext="0.56" decisive="dcytext"/>
204
- <tmsegment start="536" stop="556" prob="21.00" hp="0.82"/>
205
- <loop type="unknown" start="557" stop="854" darglys="41.00" dcytext="0.16" decisive="dcytext"/>
206
- </topology>
207
-
208
- <topology nr="4" prob="0.01" darglys="0.00" dcytext="0.25" dncharge="0.00" dnnegpos="0.12" orient="? N-out ?">
209
- <loop type="unknown" start="1" stop="408" darglys="39.00" dcytext="0.84" decisive="dcytext"/>
210
- <tmsegment start="409" stop="429" prob="21.00" hp="0.60"/>
211
- <loop type="unknown" start="430" stop="854" darglys="54.00" dcytext="0.59" decisive="dcytext"/>
212
- </topology>
213
-
214
- <topology nr="5" prob="0.01" darglys="0.00" dcytext="0.32" dncharge="0.00" dnnegpos="0.12" orient="? N-out ?">
215
- <loop type="unknown" start="1" stop="408" darglys="39.00" dcytext="0.84" decisive="dcytext"/>
216
- <tmsegment start="409" stop="429" prob="21.00" hp="0.60"/>
217
- <loop type="unknown" start="430" stop="535" darglys="13.00" dcytext="0.69" decisive="dcytext"/>
218
- <tmsegment start="536" stop="556" prob="21.00" hp="0.82"/>
219
- <loop type="unknown" start="557" stop="854" darglys="41.00" dcytext="0.16" decisive="dcytext"/>
220
- </topology>
221
-
222
- <topology nr="6" prob="0.01" darglys="0.00" dcytext="1.47" dncharge="0.00" dnnegpos="0.17" orient="? N-out ?">
223
- <loop type="unknown" start="1" stop="241" darglys="20.00" dcytext="1.10" decisive="dcytext"/>
224
- <tmsegment start="242" stop="262" prob="21.00" hp="0.68"/>
225
- <loop type="unknown" start="263" stop="408" darglys="19.00" dcytext="0.22" decisive="dcytext"/>
226
- <tmsegment start="409" stop="429" prob="21.00" hp="0.60"/>
227
- <loop type="unknown" start="430" stop="854" darglys="54.00" dcytext="0.59" decisive="dcytext"/>
228
- </topology>
229
-
230
- <topology nr="7" prob="0.01" darglys="0.00" dcytext="1.40" dncharge="0.00" dnnegpos="0.17" orient="? N-out ?">
231
- <loop type="unknown" start="1" stop="241" darglys="20.00" dcytext="1.10" decisive="dcytext"/>
232
- <tmsegment start="242" stop="262" prob="21.00" hp="0.68"/>
233
- <loop type="unknown" start="263" stop="408" darglys="19.00" dcytext="0.22" decisive="dcytext"/>
234
- <tmsegment start="409" stop="429" prob="21.00" hp="0.60"/>
235
- <loop type="unknown" start="430" stop="535" darglys="13.00" dcytext="0.69" decisive="dcytext"/>
236
- <tmsegment start="536" stop="556" prob="21.00" hp="0.82"/>
237
- <loop type="unknown" start="557" stop="854" darglys="41.00" dcytext="0.16" decisive="dcytext"/>
238
- </topology>
239
-
240
- </topologies>
241
- </toppred>
242
-
243
- <toppred>
244
- <sequence id="SWN_UBP3_HUMAN" size="863">
245
- MQRRGALFGMPGGSGGRKMAAGDIGELLVPHMPTIRVPRSGDRVYKNECAFSYDSPNSEG
246
- GLYVCMNTFLAFGREHVERHFRKTGQSVYMHLKRHAREKVRGASGGALPKRRNSKIFLDL
247
- DTDDDLNSDDYEYEDEAKLVIFPDHYEIALPNIEELPALVTIACDAVLSSKSPYRKQDPD
248
- TWENELPVSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSG
249
- GNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLAKHLAHFGIDMLHMHG
250
- TENGLQDNDIKLRVSEWEVIQESGTKLKPMYGPGYTGLKNLGNSCYLSSVMQAIFSIPEF
251
- QRAYVGNLPRIFDYSPLDPTQDFNTQMTKLGHGLLSGQYSKPPVKSELIEQVMKEEHKPQ
252
- QNGISPRMFKAFVSKSHPEFSSNRQQDAQEFFLHLVNLVERNRIGSENPSDVFRFLVEER
253
- IQCCQTRKVRYTERVDYLMQLPVAMEAATNKDELIAYELTRREAEANRRPLPELVRAKIP
254
- FSACLQAFSEPENVDDFWSSALQAKSAGVKTSRFASFPEYLVVQIKKFTFGLDWVPKKFD
255
- VSIDMPDLLDINHLRARGLQPGEEELPDISPPIVIPDDSKDRLMNQLIDPSDIDESSVMQ
256
- LAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGASVFG
257
- ASGLDNQPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHPEFEEDSDFVIEM
258
- ENNANANIISEAKPEGPRVKDGSGTYELFAFISHMGTSTMSGHYICHIKKEGRWVIYNDH
259
- KVCASERPPKDLGYMYFYRRIPS
260
- </sequence>
261
-
262
- <plot hydro="SWN_UBP3_HUMAN.hydro" gplot="SWN_UBP3_HUMAN.png"/>
263
-
264
- <tmsummary segments="3" len="21">
265
- <segment start="340" stop="360" hp="0.868" type="putative"/>
266
- <segment start="704" stop="724" hp="1.326" type="certain"/>
267
- <segment start="806" stop="826" hp="1.125" type="certain"/>
268
- </tmsummary>
269
-
270
- <topologies maxtopo="2" topoprint="2">
271
-
272
- <topology nr="1" prob="1.00" darglys="8.00" dcytext="0.63" dncharge="-1.00" dnnegpos="0.13" orient="N-in N-out N-out">
273
- <loop type="unknown" start="1" stop="703" darglys="78.00" dcytext="0.57" decisive="dcytext"/>
274
- <tmsegment start="704" stop="724" prob="21.00" hp="1.33"/>
275
- <loop type="unknown" start="725" stop="805" darglys="6.00" dcytext="-0.06" decisive="dcytext"/>
276
- <tmsegment start="806" stop="826" prob="21.00" hp="1.12"/>
277
- <loop type="unknown" start="827" stop="863" darglys="8.00" dcytext="0.60" decisive="darglys"/>
278
- </topology>
279
-
280
- <topology nr="2" prob="0.67" darglys="-8.00" dcytext="-0.06" dncharge="3.00" dnnegpos="0.11" orient="N-out N-in N-in">
281
- <loop type="unknown" start="1" stop="339" darglys="39.00" dcytext="0.41" decisive="dcytext"/>
282
- <tmsegment start="340" stop="360" prob="21.00" hp="0.87"/>
283
- <loop type="unknown" start="361" stop="703" darglys="39.00" dcytext="0.40" decisive="dcytext"/>
284
- <tmsegment start="704" stop="724" prob="21.00" hp="1.33"/>
285
- <loop type="unknown" start="725" stop="805" darglys="6.00" dcytext="-0.06" decisive="dcytext"/>
286
- <tmsegment start="806" stop="826" prob="21.00" hp="1.12"/>
287
- <loop type="unknown" start="827" stop="863" darglys="8.00" dcytext="0.60" decisive="darglys"/>
288
- </topology>
289
-
290
- </topologies>
291
- </toppred>
292
-
293
- <toppred>
294
- <sequence id="SW_FGF7_HUMAN" size="194">
295
- MHKWILTWILPTLLYRSCFHIICLVGTISLACNDMTPEQMATNVNCSSPERHTRSYDYME
296
- GGDIRVRRLFCRTQWYLRIDKRGKVKGTQEMKNNYNIMEIRTVAVGIVAIKGVESEFYLA
297
- MNKEGKLYAKKECNEDCNFKELILENHYNTYASAKWTHNGGEMFVALNQKGIPVRGKKTK
298
- KEQKTAHFLPMAIT
299
- </sequence>
300
-
301
- <plot hydro="SW_FGF7_HUMAN.hydro" gplot="SW_FGF7_HUMAN.png"/>
302
-
303
- <tmsummary segments="1" len="21">
304
- <segment start="16" stop="36" hp="1.139" type="certain"/>
305
- </tmsummary>
306
-
307
- <topologies maxtopo="1" topoprint="1">
308
-
309
- <topology nr="1" prob="1.00" darglys="3.00" dcytext="-0.16" dncharge="5.00" dnnegpos="-1.00" orient="N-in N-in N-in">
310
- <loop type="unknown" start="1" stop="15" darglys="2.00" dcytext="0.02" decisive="darglys"/>
311
- <tmsegment start="16" stop="36" prob="21.00" hp="1.14"/>
312
- <loop type="unknown" start="37" stop="194" darglys="27.00" dcytext="0.16" decisive="dcytext"/>
313
- </topology>
314
-
315
- </topologies>
316
- </toppred>
317
-
318
- </toppreds>
data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta DELETED
@@ -1,7 +0,0 @@
1
- >gi|16130902|ref|NP_417477.1| unknown CDS [Escherichia coli K12]
2
- >gi|16128499|ref|NP_415048.1| hypothetical protein b0515 [Escherichia coli K12]
3
- >gi|90111171|ref|NP_415327.2| hypothetical protein b0806 [Escherichia coli K12]
4
- >gi|90111191|ref|NP_415463.2| putative fimbrial-like protein [Escherichia coli K12]
5
- >gi|16130905|ref|NP_417480.1| unknown CDS [Escherichia coli K12]
6
- >gi|49176253|ref|YP_026176.1| CP4-57 prophage [Escherichia coli K12]
7
- >gi|16129488|ref|NP_416046.1| multiple antibiotic resistance protein [Escherichia coli K12]