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/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">
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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
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+ 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
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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
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+ ITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEDGLVQLETVNLQVA
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+ TYSKSKFCYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSADFLDITNPKAVLEN
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+ 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"/>
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+
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+ <tmsummary segments="0">
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+ </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]