mspire 0.2.4 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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/toppred.xml.out ADDED
@@ -0,0 +1,318 @@
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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">
19
+ MNRSRQVTCVAWVRCGVAKETPDKVELSKEEVKRLIAEAKEKLQEEGGGSDEEETGSPSE
20
+ DGMQSARTQARPREPLEDGDPEDDRTLDDDELAEYDLDKYDEEGDPDAETLGESLLGLTV
21
+ YGSNDQDPYVTLKDTEQYEREDFLIKPSDNLIVCGRAEQDQCNLEVHVYNQEEDSFYVHH
22
+ DILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWDLDIVDSLEPVFTLGSKLSK
23
+ KKKKKGKKSSSAEGHTDAVLDLSWNKLIRNVLASASADNTVILWDMSLGKPAASLAVHTD
24
+ KVQTLQFHPFEAQTLISGSYDKSVALYDCRSPDESHRMWRFSGQIERVTWNHFSPCHFLA
25
+ 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
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+ </sequence>
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+
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+ <plot hydro="SWN_UBCE_HUMAN.hydro" gplot="SWN_UBCE_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_UFD1_HUMAN" size="343">
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+ MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAWPNDRSDVEKGGKIIMPPSALDQLSRLN
110
+ ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEDGLVQLETVNLQVA
111
+ TYSKSKFCYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSADFLDITNPKAVLEN
112
+ ALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIHECDMNVDFDAPLGYKEPERQV
113
+ QHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFK
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+ LGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSLRKKGRKP
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+ </sequence>
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+
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+ <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 ADDED
@@ -0,0 +1,7 @@
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]