miga-base 1.2.17.0 → 1.2.17.1

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Files changed (299) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/version.rb +1 -1
  3. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
  4. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
  5. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
  6. data/utils/FastAAI/FastAAI +3659 -0
  7. data/utils/FastAAI/FastAAI-legacy/FastAAI +1336 -0
  8. data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +1296 -0
  9. data/utils/FastAAI/README.md +84 -0
  10. data/utils/enveomics/Docs/recplot2.md +244 -0
  11. data/utils/enveomics/Examples/aai-matrix.bash +66 -0
  12. data/utils/enveomics/Examples/ani-matrix.bash +66 -0
  13. data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
  14. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
  15. data/utils/enveomics/LICENSE.txt +73 -0
  16. data/utils/enveomics/Makefile +52 -0
  17. data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
  18. data/utils/enveomics/Manifest/Tasks/blasttab.json +790 -0
  19. data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
  20. data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
  21. data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
  22. data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
  23. data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
  24. data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
  25. data/utils/enveomics/Manifest/Tasks/other.json +906 -0
  26. data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
  27. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +650 -0
  28. data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
  29. data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
  30. data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
  31. data/utils/enveomics/Manifest/categories.json +165 -0
  32. data/utils/enveomics/Manifest/examples.json +162 -0
  33. data/utils/enveomics/Manifest/tasks.json +4 -0
  34. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
  35. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
  36. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
  37. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
  38. data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
  39. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
  40. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
  41. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
  42. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
  43. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
  44. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
  45. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
  46. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
  47. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
  48. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
  49. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
  50. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
  51. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
  52. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
  53. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
  54. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
  55. data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
  56. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
  57. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
  58. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
  59. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
  60. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
  61. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
  62. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
  63. data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
  64. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
  65. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
  66. data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
  67. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
  68. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
  69. data/utils/enveomics/README.md +42 -0
  70. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  71. data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
  72. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  73. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  74. data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
  75. data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
  76. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  77. data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
  78. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  79. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  80. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
  81. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  82. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  83. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  84. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  85. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  86. data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
  87. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  88. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  89. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  90. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  91. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  92. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  93. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
  94. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  95. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  96. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  97. data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
  98. data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
  99. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  100. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  101. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  102. data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
  103. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  104. data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
  105. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  106. data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
  107. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  108. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  109. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  110. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  111. data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
  112. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  113. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  114. data/utils/enveomics/Scripts/FastA.split.rb +79 -0
  115. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  116. data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
  117. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  118. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  119. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  120. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  121. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  122. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  123. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  124. data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
  125. data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
  126. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  127. data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
  128. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  129. data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
  130. data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
  131. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  132. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  133. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
  134. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  135. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  136. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  137. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  138. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  139. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  140. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  141. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
  142. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  143. data/utils/enveomics/Scripts/SRA.download.bash +55 -0
  144. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  145. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  146. data/utils/enveomics/Scripts/Table.barplot.R +31 -0
  147. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  148. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  149. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  150. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  151. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  152. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  153. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  154. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  155. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  156. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  157. data/utils/enveomics/Scripts/aai.rb +421 -0
  158. data/utils/enveomics/Scripts/ani.rb +362 -0
  159. data/utils/enveomics/Scripts/anir.rb +137 -0
  160. data/utils/enveomics/Scripts/clust.rand.rb +102 -0
  161. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  162. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  163. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  164. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  165. data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
  166. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  167. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  168. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
  169. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  170. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  171. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  172. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
  173. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  174. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  175. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  176. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  177. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  178. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  179. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  180. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  182. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  183. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  184. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  185. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  186. data/utils/enveomics/Scripts/ogs.rb +104 -0
  187. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  188. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  189. data/utils/enveomics/Scripts/rbm.rb +108 -0
  190. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  191. data/utils/enveomics/Tests/Makefile +10 -0
  192. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  193. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  194. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  195. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  196. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  197. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  198. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  199. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  200. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  201. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  202. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  203. data/utils/enveomics/Tests/alkB.nwk +1 -0
  204. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  205. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  206. data/utils/enveomics/Tests/hiv1.faa +59 -0
  207. data/utils/enveomics/Tests/hiv1.fna +134 -0
  208. data/utils/enveomics/Tests/hiv2.faa +70 -0
  209. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  210. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  211. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  212. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  213. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  214. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  215. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  216. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  217. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  218. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  219. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  220. data/utils/enveomics/build_enveomics_r.bash +45 -0
  221. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  222. data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
  223. data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
  224. data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
  225. data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
  226. data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
  227. data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
  228. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  229. data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
  230. data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
  231. data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
  232. data/utils/enveomics/enveomics.R/R/utils.R +80 -0
  233. data/utils/enveomics/enveomics.R/README.md +81 -0
  234. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  235. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  236. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
  237. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
  238. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
  239. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
  240. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
  241. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
  242. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
  243. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
  244. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
  245. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
  246. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
  247. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
  248. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
  249. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
  250. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
  251. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
  252. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
  253. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
  254. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
  255. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
  256. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
  257. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
  258. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
  259. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
  260. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
  261. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
  262. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
  263. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
  264. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
  280. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
  281. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
  282. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
  283. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
  284. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  285. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  286. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
  287. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
  288. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
  289. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
  290. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
  291. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
  292. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
  293. data/utils/enveomics/globals.mk +8 -0
  294. data/utils/enveomics/manifest.json +9 -0
  295. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  296. data/utils/multitrim/README.md +67 -0
  297. data/utils/multitrim/multitrim.py +1555 -0
  298. data/utils/multitrim/multitrim.yml +13 -0
  299. metadata +301 -5
data/utils/enveomics/Tests/hiv1.faa ADDED
@@ -0,0 +1,59 @@
1
+ >lcl|AF033819.3_prot_AAC82593.1_1 [gene=gag] [protein=Gag] [protein_id=AAC82593.1] [location=336..1838]
2
+ MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQT
3
+ GSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQG
4
+ QMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA
5
+ EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPT
6
+ SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTAC
7
+ QGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEG
8
+ HQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLR
9
+ SLFGNDPSSQ
10
+ >lcl|AF033819.3_prot_AAC82598.2_2 [gene=pol] [protein=Pol] [partial=5'] [protein_id=AAC82598.2] [location=<1631..4642]
11
+ FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIK
12
+ IGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNI
13
+ IGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENP
14
+ YNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFR
15
+ KYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEI
16
+ GQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLN
17
+ WASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQG
18
+ QWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
19
+ WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
20
+ KTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGN
21
+ EQVDKLVSAGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD
22
+ CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGAT
23
+ VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYS
24
+ AGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKA
25
+ KIIRDYGKQMAGDDCVASRQDED
26
+ >lcl|AF033819.3_prot_AAC82594.1_3 [gene=vif] [protein=Vif] [protein_id=AAC82594.1] [location=4587..5165]
27
+ MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLGDARLVITTYW
28
+ GLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHN
29
+ KVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH
30
+ >lcl|AF033819.3_prot_AAC82595.1_4 [gene=vpr] [protein=Vpr] [protein_id=AAC82595.1] [location=5105..5341]
31
+ MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQHIYETYGDTWAGVEAIIRILQQLLFI
32
+ HFQNWVST
33
+ >lcl|AF033819.3_prot_AAC82591.1_5 [gene=tat] [protein=Tat] [protein_id=AAC82591.1] [location=join(5377..5591,7925..7970)]
34
+ MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGRKKRRQRRRAHQNSQTHQASLS
35
+ KQPTSQPRGDPTGPKE
36
+ >lcl|AF033819.3_prot_AAC82592.1_6 [gene=rev] [protein=Rev] [protein_id=AAC82592.1] [location=join(5516..5591,7925..8199)]
37
+ MAGRSGDSDEELIRTVRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQIHSISERILGTYLGRSAEP
38
+ VPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESPTVLESGTKE
39
+ >lcl|AF033819.3_prot_AAD20388.1_7 [gene=vpu] [protein=Vpu] [protein_id=AAD20388.1] [location=5608..5856]
40
+ MQPIPIVAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVEMGVE
41
+ MGHHAPWDVDDL
42
+ >lcl|AF033819.3_prot_AAC82596.1_8 [gene=env] [protein=Env] [protein_id=AAC82596.1] [location=5771..8341]
43
+ MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWA
44
+ THACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNT
45
+ NSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSF
46
+ EPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDN
47
+ AKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLR
48
+ EQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRI
49
+ KQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVK
50
+ IEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIE
51
+ AQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWME
52
+ WDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFA
53
+ VLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHR
54
+ LRDLLLIVTRIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAI
55
+ RHIPRRIRQGLERILL
56
+ >lcl|AF033819.3_prot_AAC82597.1_9 [gene=nef] [protein=Nef] [protein_id=AAC82597.1] [location=8343..8714]
57
+ MGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPV
58
+ TPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPD
59
+
data/utils/enveomics/Tests/hiv1.fna ADDED
@@ -0,0 +1,134 @@
1
+ >gi|4558520|gb|AF033819.3| HIV-1, complete genome
2
+ GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCC
3
+ TCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGA
4
+ TCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAA
5
+ AGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGG
6
+ CGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCG
7
+ TCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAAT
8
+ ATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGA
9
+ AACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTT
10
+ AGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGG
11
+ AAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACAC
12
+ AGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAG
13
+ GCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGA
14
+ TACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGG
15
+ GGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTG
16
+ CATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAA
17
+ CTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTA
18
+ TAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATA
19
+ AGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAG
20
+ CTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGAC
21
+ TATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGA
22
+ CCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGC
23
+ AGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGC
24
+ CAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGAT
25
+ TGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTC
26
+ TTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCC
27
+ CCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAAC
28
+ GACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATAC
29
+ AGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATC
30
+ AAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAG
31
+ GACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCAT
32
+ TAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCA
33
+ TTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAA
34
+ AAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAG
35
+ AAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCA
36
+ CATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTC
37
+ CCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGAT
38
+ TAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACA
39
+ AAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATG
40
+ TAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTG
41
+ GGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCAT
42
+ CCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGA
43
+ AGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACT
44
+ CCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAA
45
+ AACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAA
46
+ TACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGG
47
+ AAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATA
48
+ ACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGG
49
+ AAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTT
50
+ AGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCA
51
+ GCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCC
52
+ TAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGA
53
+ AGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCA
54
+ GAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCAC
55
+ ACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTT
56
+ AGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGAT
57
+ TTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAG
58
+ CCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGT
59
+ TATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAG
60
+ GAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCA
61
+ GCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCC
62
+ CTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTA
63
+ AGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAG
64
+ GGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGA
65
+ ATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGG
66
+ AAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAG
67
+ TAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGC
68
+ AAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGC
69
+ TAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCA
70
+ CTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGG
71
+ GTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCA
72
+ ACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATA
73
+ GTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAG
74
+ CATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAA
75
+ CAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGC
76
+ TTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAAC
77
+ TTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTT
78
+ CAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGA
79
+ TCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAA
80
+ AAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGC
81
+ GGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGT
82
+ ACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTT
83
+ GTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATA
84
+ GACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGG
85
+ GGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCAC
86
+ AGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCA
87
+ TATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAG
88
+ TAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGA
89
+ TATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAG
90
+ TGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGA
91
+ TAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTA
92
+ TAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTC
93
+ ATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTG
94
+ CGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATG
95
+ TACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTA
96
+ GTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAA
97
+ TTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATT
98
+ TGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAAC
99
+ ACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAAT
100
+ CCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTC
101
+ AACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGA
102
+ AGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAA
103
+ TGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGA
104
+ TGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGA
105
+ AGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAA
106
+ GAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGG
107
+ AAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAG
108
+ CAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCA
109
+ AGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGG
110
+ TTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAA
111
+ CAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACT
112
+ CCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGC
113
+ AAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGA
114
+ GGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCAC
115
+ CATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGG
116
+ TGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTG
117
+ CGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAAC
118
+ TTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACT
119
+ AAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATA
120
+ GAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGA
121
+ TTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAA
122
+ TGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAAT
123
+ CACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTG
124
+ GGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACT
125
+ TTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTG
126
+ GATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCA
127
+ CTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAG
128
+ AGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTG
129
+ GAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC
130
+ TGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTG
131
+ GGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAG
132
+ ACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCC
133
+ TTGAGTGCTTC
134
+
data/utils/enveomics/Tests/hiv2.faa ADDED
@@ -0,0 +1,70 @@
1
+ >lcl|NC_001722.1_prot_NP_663784.1_1 [gene=gag-pol] [protein=gag-pol fusion polyprotein] [protein_id=NP_663784.1] [location=join(1103..2398,2398..5754)]
2
+ MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKILRVLDPLVPT
3
+ GSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQA
4
+ GGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEE
5
+ AADWDSQHPIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYN
6
+ PTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLT
7
+ ACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
8
+ IMANCPERQAGFFRVGPTGKEASQLPRDPSPSGADTNSTSGRSSSGTVGEIYAAREKAEGAEGETIQRGD
9
+ GGLAAPRAERDTSQRGDRGLAAPQFSLWKRPVVTAYIEDQPVEVLLDTGADDSIVAGIELGDNYTPKIVG
10
+ GIGGFINTKEYKNVEIKVLNKRVRATIMTGDTPINIFGRNILTALGMSLNLPVAKIEPIKVTLKPGKDGP
11
+ RLKQWPLTKEKIEALKEICEKMEKEGQLEEAPPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVTQDFTE
12
+ IQLGIPHPAGLAKKKRISILDVGDAYFSIPLHEDFRQYTAFTLPAVNNMEPGKRYIYKVLPQGWKGSPAI
13
+ FQYTMRQVLEPFRKANPDVILIQYMDDILIASDRTGLEHDKVVLQLKELLNGLGFSTPDEKFQKDPPFQW
14
+ MGCELWPTKWKLQKLQLPQKDIWTVNDIQKLVGVLNWAAQIYSGIKTKHLCRLIRGKMTLTEEVQWTELA
15
+ EAELEENKIILSQEQEGYYYQEEKELEATIQKSQGHQWTYKIHQEEKILKVGKYAKIKNTHTNGVRLLAQ
16
+ VVQKIGKEALVIWGRIPKFHLPVERETWEQWWDNYWQVTWIPEWDFVSTPPLVRLTFNLVGDPIPGAETF
17
+ YTDGSCNRQSKEGKAGYVTDRGKDKVKVLEQTTNQQAELEVFRMALADSGPKVNIIVDSQYVMGIVAGQP
18
+ TESENRIVNQIIEEMIKKEAVYVAWVPAHKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHSIIK
19
+ ELTHKFGIPLLVARQIVNSCAQCQQKGEAIHGQVNAEIGVWQMDYTHLEGKIIIVAVHVASGFIEAEVIP
20
+ QESGRQTALFLLKLASRWPITHLHTDNGPNFTSQEVKMVAWWVGIEQSFGVPYNPQSQGVVEAMNHHLKN
21
+ QISRIREQANTIETIVLMAVHCMNFKRRGGIGDMTPAERLINMITTEQEIQFLQRKNSNFKNFQVYYREG
22
+ RDQLWKGPGELLWKGEGAVIVKVGTDIKVVPRRKAKIIRDYGGRQELDSSPHLEGAREDGEMACPCQVPE
23
+ IQNKRPRGGALCSPPQGGMGMVDLQQGNIPTTRKKSSRNTGILEPNTRKRMALLSCSKINLVYRKVLDRC
24
+ YPRLCRHPNT
25
+ >lcl|NC_001722.1_prot_NP_056837.1_2 [gene=gag-pol] [protein=gag polyprotein] [protein_id=NP_056837.1] [location=1103..2668]
26
+ MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKILRVLDPLVPT
27
+ GSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPNTSRPTAPPSGKRGNYPVQQA
28
+ GGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEE
29
+ AADWDSQHPIPGPLPAGQLRDPRGSDIAGTTSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYN
30
+ PTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLT
31
+ ACQGVGGPGQKARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
32
+ IMANCPERQAGFLGLGPRGKKPRNFPVTQAPQGLIPTAPPADPAAELLERYMQQGRKQREQRERPYKEVT
33
+ EDLLHLEQRETPHREETEDLLHLNSLFGKDQ
34
+ >lcl|NC_001722.1_prot_NP_056839.1_3 [gene=HIV2gp2] [protein=vif protein] [protein_id=NP_056839.1] [location=5423..6070]
35
+ MEEDRNWIVVPTWRVPGRMEKWHALVKYLKYRTKDLEEVRYVPHHKVGWAWWTCSRVIFPLQGKSHLEIQ
36
+ AYWNLTPEKGWLSSHAVRLTWYTEKFWTDVTPDCADILIHSTYFSCFTAGEVRRAIRGEKLLSCCNYPQA
37
+ HKAQVPSLQYLALVVVQQNDRPQRKGTARKQWRRDHWRGLRVAREDHRSLKQGGSEPSAPRAHFPGVAKV
38
+ LEILA
39
+ >lcl|NC_001722.1_prot_NP_056840.1_4 [gene=HIV2gp3] [protein=vpx protein] [protein_id=NP_056840.1] [location=5898..6239]
40
+ MTDPRERVPPGNSGEETIGEAFEWLERTIEALNREAVNHLPRELIFQVWQRSWRYWHDEQGMSASYTKYR
41
+ YLCLMQKAIFTHFKRGCTCWGEDMGREGLEDQGPPPPPPPGLV
42
+ >lcl|NC_001722.1_prot_NP_056841.1_5 [gene=HIV2gp4] [protein=vpr protein] [protein_id=NP_056841.1] [location=6239..6502]
43
+ MTEAPTEFPPEDGTPRRDLGSDWVIETLREIKEEALRHFDPRLLIALGYYIHNRHGDTLEGARELIKTLQ
44
+ RALFVHFRAGCNRSRIG
45
+ >lcl|NC_001722.1_prot_NP_056842.1_6 [gene=HIV2gp5] [protein=tat protein] [protein_id=NP_056842.1] [location=join(6402..6697,8861..8957)]
46
+ METPLKAPESSLKPYNEPSSCTSERDVTAQELAKQGEELLAQLHRPLEPCTNKCYCKRCSFHCQLCFSKK
47
+ GLGISYERKGRRRRTPRKTKTPSPSAPDKSISTRTGDSQPTKEQKKTSEATVVTTCGLGQ
48
+ >lcl|NC_001722.1_prot_NP_056843.1_7 [gene=HIV2gp6] [protein=rev protein] [protein_id=NP_056843.1] [location=join(6628..6697,8861..9102)]
49
+ MSERADEEGLQGKLRLLRLLHQTNPYPQGPGTASQRRNRRRRRRRQWLRLVALANKLCAVPDPPTDSPLD
50
+ RAIQHLQRLTIQELPDPPTDLPESNSNQGLAET
51
+ >lcl|NC_001722.1_prot_NP_056844.1_8 [gene=HIV2gp7] [protein=env polyprotein] [protein_id=NP_056844.1] [location=6704..9286]
52
+ MEPGRNQLFVVILLTSACLVYCSQYVTVFYGIPAWKNASIPLFCATKNRDTWGTIQCLPDNDDYQEIILN
53
+ VTEAFDAWNNTVTEQAVEDVWHLFETSIKPCVKLTPLCVAMNCSRVQGNTTTPNPRTSSSTTSRPPTSAA
54
+ SIINETSNCIENNTCAGLGYEEMMQCEFNMKGLEQDKKRRYKDTWYLEDVVCDNTTAGTCYMRHCNTSII
55
+ KESCDKHYWDAMRFRYCAPPGFALLRCNDTNYSGFEPKCTKVVAASCTRMMETQTSTWFGFNGTRAENRT
56
+ YIYWHGRDNRTIISLNKYYNLTMRCKRPGNKTVLPITLMSGLVFHSQPINTRPRQAWCRFGGRWREAMQE
57
+ VKQTLVQHPRYKGINDTGKINFTKPGAGSDPEVAFMWTNCRGEFLYCNMTWFLNWVEDKNQTRRNYCHIK
58
+ QIINTWHKVGKNVYLPPREGELACESTVTSIIANIDIDKNRTHTNITFSAEVAELYRLELGDYKLIEITP
59
+ IGFAPTDQRRYSSTPVRNKRGVFVLGFLGFLATAGSAMGARSLTLSAQSRTLLAGIVQQQQQLLDVVKRQ
60
+ QEMLRLTVWGTKNLQARVTAIEKYLKHQAQLNSWGCAFRQVCHTTVPWVNDSLSPDWKNMTWQEWEKQVR
61
+ YLEANISQSLEEAQIQQEKNMYELQKLNSWDILGNWFDLTSWVKYIQYGVHIVVGIIALRIAIYVVQLLS
62
+ RFRKGYRPVFSSPPGYLQQIHIHKDRGQPANEGTEEDVGGDSGYDLWPWPINYVQFLIHLLTRLLIGLYN
63
+ ICRDLLSKNSPTRRLISQSLTAIRDWLRLKAAQLQYGCEWIQEAFQAFARTTRETLAGAWGWLWEAARRI
64
+ GRGILAVPRRIRQGAELALL
65
+ >lcl|NC_001722.1_prot_NP_056845.1_9 [gene=HIV2gp8] [protein=nef protein] [protein_id=NP_056845.1] [location=9120..9893]
66
+ MGASGSKKLSKHSRGLRERLLRARGDGYGKQRDASGGEYSQFQEESGREQNSPSCEGQQYQQGEYMNSPW
67
+ RNPATERQKDLYRQQNMDDVDSDDDDLIGVPVTPRVPRREMTYKLAIDMSHFIKEKGGLQGMFYSRRRHR
68
+ ILDIYLEKEEGIIPDWQNYTHGPGVRYPMYFGWLWKLVSVELSQEAEEDEANCLVHPAQTSRHDDEHGET
69
+ LVWQFDSMLAYNYKAFTLYPEEFGHKSGLPEKEWKAKLKARGIPYSE
70
+
data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv ADDED
@@ -0,0 +1,233 @@
1
+ 2 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 8626 8527 1e-45 169
2
+ 3 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4499 4598 1e-40 152
3
+ 6 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 553 652 2e-43 161
4
+ 9 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 5662 5563 4e-39 147
5
+ 12 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 1541 1640 2e-42 158
6
+ 14 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4742 4841 1e-40 152
7
+ 17 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2564 2663 3e-41 154
8
+ 18 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7821 7722 2e-43 161
9
+ 19 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2559 2460 3e-41 154
10
+ 23 gi|4558520|gb|AF033819.3| 96.94 98 1 2 4 100 7816 7912 4e-44 163
11
+ 25 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 8552 8648 4e-44 163
12
+ 28 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 309 213 4e-44 163
13
+ 33 gi|4558520|gb|AF033819.3| 94.12 102 4 2 1 102 2601 2700 3e-41 154
14
+ 34 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 2184 2085 1e-45 169
15
+ 35 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 3495 3396 3e-40 150
16
+ 40 gi|4558520|gb|AF033819.3| 93.94 99 5 1 1 99 1429 1332 1e-39 148
17
+ 44 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 6500 6599 1e-45 169
18
+ 46 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 771 672 4e-44 163
19
+ 47 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 6089 6188 2e-42 158
20
+ 48 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 315 414 4e-44 163
21
+ 49 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 4928 4829 1e-45 169
22
+ 50 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 4023 3924 7e-42 156
23
+ 51 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 6570 6471 2e-42 158
24
+ 52 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 5494 5395 2e-42 158
25
+ 55 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1056 957 4e-44 163
26
+ 56 gi|4558520|gb|AF033819.3| 93.94 99 4 2 1 98 6840 6743 1e-39 148
27
+ 58 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 6072 5973 4e-44 163
28
+ 60 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 5866 5965 1e-40 152
29
+ 63 gi|4558520|gb|AF033819.3| 96.97 99 3 0 1 99 5535 5437 3e-45 167
30
+ 65 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 7136 7235 1e-45 169
31
+ 66 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 5001 5100 4e-44 163
32
+ 68 gi|4558520|gb|AF033819.3| 94.90 98 5 0 1 98 8605 8508 3e-41 154
33
+ 70 gi|4558520|gb|AF033819.3| 97.98 99 1 1 1 98 8063 7965 3e-46 171
34
+ 71 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 1899 1998 1e-39 148
35
+ 72 gi|4558520|gb|AF033819.3| 93.07 101 6 1 1 101 7652 7553 5e-39 147
36
+ 73 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 7407 7506 1e-40 152
37
+ 75 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 9169 9070 4e-44 163
38
+ 75 gi|4558520|gb|AF033819.3| 95.24 84 4 0 1 84 84 1 3e-35 134
39
+ 76 gi|4558520|gb|AF033819.3| 96.00 100 2 2 1 98 3393 3294 2e-43 161
40
+ 79 gi|4558520|gb|AF033819.3| 94.12 102 3 3 1 101 166 67 1e-40 152
41
+ 81 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 2902 3001 3e-40 150
42
+ 85 gi|4558520|gb|AF033819.3| 94.00 100 4 2 1 98 7979 8078 3e-40 150
43
+ 86 gi|4558520|gb|AF033819.3| 96.00 100 2 2 3 102 3221 3124 2e-43 161
44
+ 87 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 8311 8410 1e-40 152
45
+ 91 gi|4558520|gb|AF033819.3| 97.92 96 2 0 1 96 3809 3904 3e-45 167
46
+ 97 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8815 8914 7e-42 156
47
+ 100 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 3563 3464 2e-42 158
48
+ 109 gi|4558520|gb|AF033819.3| 96.04 101 2 2 1 100 6572 6671 4e-44 163
49
+ 110 gi|4558520|gb|AF033819.3| 93.20 103 4 3 1 102 7432 7532 1e-39 148
50
+ 112 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8628 8529 7e-42 156
51
+ 113 gi|4558520|gb|AF033819.3| 94.85 97 3 2 1 96 1001 1096 3e-40 150
52
+ 114 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 207 108 7e-42 156
53
+ 116 gi|4558520|gb|AF033819.3| 95.96 99 4 0 1 99 4408 4310 2e-43 161
54
+ 117 gi|4558520|gb|AF033819.3| 96.91 97 2 1 3 98 2591 2687 2e-43 161
55
+ 122 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 4430 4529 1e-40 152
56
+ 123 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 6771 6867 4e-44 163
57
+ 125 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 868 967 3e-40 150
58
+ 126 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 8524 8623 2e-47 174
59
+ 127 gi|4558520|gb|AF033819.3| 93.88 98 6 0 1 98 4858 4761 1e-39 148
60
+ 128 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3091 3190 1e-45 169
61
+ 132 gi|4558520|gb|AF033819.3| 97.96 98 2 0 1 98 2864 2767 3e-46 171
62
+ 138 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 3780 3879 3e-40 150
63
+ 143 gi|4558520|gb|AF033819.3| 95.88 97 4 0 1 97 389 485 2e-42 158
64
+ 147 gi|4558520|gb|AF033819.3| 94.90 98 5 0 1 98 7601 7698 3e-41 154
65
+ 148 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 4224 4125 2e-38 145
66
+ 151 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7072 6973 1e-45 169
67
+ 152 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 871 967 1e-45 169
68
+ 153 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6419 6320 2e-42 158
69
+ 157 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 7988 7889 4e-44 163
70
+ 159 gi|4558520|gb|AF033819.3| 97.98 99 2 0 1 99 7249 7347 7e-47 172
71
+ 164 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 6862 6961 1e-39 148
72
+ 165 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 4350 4251 2e-43 161
73
+ 166 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 5519 5420 1e-40 152
74
+ 167 gi|4558520|gb|AF033819.3| 94.00 100 4 2 1 98 1996 2095 3e-40 150
75
+ 168 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 6319 6220 7e-42 156
76
+ 169 gi|4558520|gb|AF033819.3| 99.00 100 0 1 1 99 4211 4310 2e-48 178
77
+ 170 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 101 258 160 2e-42 158
78
+ 172 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1835 1934 2e-43 161
79
+ 173 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 4744 4645 4e-39 147
80
+ 175 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 2245 2344 7e-42 156
81
+ 177 gi|4558520|gb|AF033819.3| 92.08 101 7 1 1 101 4239 4140 2e-37 141
82
+ 181 gi|4558520|gb|AF033819.3| 94.12 102 2 4 1 100 7812 7713 1e-40 152
83
+ 185 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 2859 2760 7e-42 156
84
+ 189 gi|4558520|gb|AF033819.3| 96.00 100 2 2 1 98 2328 2427 2e-43 161
85
+ 191 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 1049 950 1e-40 152
86
+ 193 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6925 7024 2e-42 158
87
+ 195 gi|4558520|gb|AF033819.3| 92.00 100 6 2 1 99 3189 3091 7e-37 139
88
+ 196 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 7156 7057 3e-40 150
89
+ 198 gi|4558520|gb|AF033819.3| 95.00 100 3 2 1 98 8894 8993 7e-42 156
90
+ 199 gi|4558520|gb|AF033819.3| 95.05 101 2 3 1 99 5526 5427 7e-42 156
91
+ 200 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 6101 6002 3e-40 150
92
+ 205 gi|4558520|gb|AF033819.3| 96.91 97 3 0 1 97 799 703 4e-44 163
93
+ 206 gi|4558520|gb|AF033819.3| 96.08 102 2 2 1 102 6278 6179 1e-44 165
94
+ 207 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1539 1440 4e-44 163
95
+ 210 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 100 4363 4461 3e-40 150
96
+ 211 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 3274 3373 2e-42 158
97
+ 213 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 2528 2429 1e-45 169
98
+ 215 gi|4558520|gb|AF033819.3| 95.05 101 3 2 1 100 2692 2593 2e-42 158
99
+ 217 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 3875 3974 3e-45 167
100
+ 219 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1301 1202 2e-43 161
101
+ 221 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 2219 2318 2e-47 174
102
+ 223 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 9052 9151 7e-42 156
103
+ 223 gi|4558520|gb|AF033819.3| 93.94 66 3 1 35 99 1 66 1e-24 99.0
104
+ 225 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 5238 5337 2e-42 158
105
+ 228 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 2779 2878 1e-40 152
106
+ 230 gi|4558520|gb|AF033819.3| 92.93 99 7 0 1 99 422 520 2e-38 145
107
+ 231 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 272 371 2e-42 158
108
+ 233 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 4096 4195 2e-42 158
109
+ 234 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 7223 7322 4e-39 147
110
+ 237 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 8572 8473 1e-45 169
111
+ 238 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5713 5614 4e-44 163
112
+ 239 gi|4558520|gb|AF033819.3| 95.88 97 4 0 1 97 8899 8803 2e-42 158
113
+ 240 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 6817 6718 2e-42 158
114
+ 242 gi|4558520|gb|AF033819.3| 94.85 97 3 2 1 95 5361 5457 3e-40 150
115
+ 251 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 865 964 1e-40 152
116
+ 253 gi|4558520|gb|AF033819.3| 92.00 100 7 1 1 99 8540 8441 7e-37 139
117
+ 254 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 7072 7171 1e-40 152
118
+ 255 gi|4558520|gb|AF033819.3| 91.00 100 9 0 1 100 1579 1678 1e-35 135
119
+ 256 gi|4558520|gb|AF033819.3| 95.92 98 3 1 1 97 4699 4602 2e-42 158
120
+ 260 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 617 518 3e-45 167
121
+ 261 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3212 3311 1e-45 169
122
+ 264 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 9066 8967 4e-44 163
123
+ 270 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 6604 6508 9e-46 169
124
+ 271 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7747 7648 2e-43 161
125
+ 273 gi|4558520|gb|AF033819.3| 93.27 104 3 4 1 104 8331 8430 4e-40 150
126
+ 274 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 7707 7806 1e-40 152
127
+ 275 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 6754 6853 3e-45 167
128
+ 277 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 8802 8703 1e-45 169
129
+ 278 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 5040 4941 2e-43 161
130
+ 280 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 925 1024 2e-43 161
131
+ 284 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 212 311 1e-40 152
132
+ 285 gi|4558520|gb|AF033819.3| 96.94 98 3 0 1 98 5882 5979 1e-44 165
133
+ 287 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 3426 3525 4e-39 147
134
+ 288 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 6897 6996 1e-45 169
135
+ 290 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 492 591 2e-42 158
136
+ 295 gi|4558520|gb|AF033819.3| 94.95 99 4 1 3 101 5246 5343 3e-41 154
137
+ 297 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 1240 1141 4e-44 163
138
+ 298 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 100 934 836 3e-45 167
139
+ 301 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 5086 5185 2e-38 145
140
+ 302 gi|4558520|gb|AF033819.3| 94.90 98 4 1 4 101 9114 9018 1e-40 152
141
+ 303 gi|4558520|gb|AF033819.3| 96.88 96 2 1 1 96 8526 8620 6e-43 159
142
+ 305 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 9066 9165 7e-42 156
143
+ 305 gi|4558520|gb|AF033819.3| 95.00 80 3 1 21 99 1 80 2e-32 124
144
+ 307 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 3263 3164 1e-40 152
145
+ 313 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 2302 2401 2e-42 158
146
+ 315 gi|4558520|gb|AF033819.3| 94.00 100 5 1 1 99 6651 6552 3e-40 150
147
+ 316 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 4702 4801 4e-44 163
148
+ 319 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5363 5462 4e-44 163
149
+ 320 gi|4558520|gb|AF033819.3| 97.98 99 2 0 1 99 4305 4403 7e-47 172
150
+ 321 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 2970 3069 2e-42 158
151
+ 322 gi|4558520|gb|AF033819.3| 97.03 101 2 1 1 101 3651 3750 1e-45 169
152
+ 323 gi|4558520|gb|AF033819.3| 93.00 100 5 2 1 98 9070 8971 2e-38 145
153
+ 325 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7301 7400 2e-43 161
154
+ 326 gi|4558520|gb|AF033819.3| 94.06 101 3 3 1 99 1641 1542 3e-40 150
155
+ 332 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 6132 6033 2e-47 174
156
+ 333 gi|4558520|gb|AF033819.3| 93.48 92 5 1 1 91 5053 4962 1e-35 135
157
+ 335 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 5201 5102 1e-40 152
158
+ 336 gi|4558520|gb|AF033819.3| 92.71 96 7 0 2 97 1001 1096 8e-37 139
159
+ 338 gi|4558520|gb|AF033819.3| 93.14 102 5 2 1 102 3105 3006 1e-39 148
160
+ 339 gi|4558520|gb|AF033819.3| 95.92 98 3 1 1 97 5754 5657 2e-42 158
161
+ 342 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 829 928 1e-40 152
162
+ 343 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 7077 6978 4e-39 147
163
+ 344 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 100 3925 4024 1e-40 152
164
+ 345 gi|4558520|gb|AF033819.3| 95.96 99 3 1 1 98 2046 2144 6e-43 159
165
+ 353 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7951 8050 2e-42 158
166
+ 354 gi|4558520|gb|AF033819.3| 96.81 94 3 0 1 94 9110 9017 2e-42 158
167
+ 355 gi|4558520|gb|AF033819.3| 91.09 101 8 1 1 101 5507 5606 1e-35 135
168
+ 362 gi|4558520|gb|AF033819.3| 93.07 101 5 2 1 100 5709 5808 4e-39 147
169
+ 363 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 6394 6295 1e-40 152
170
+ 368 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 6553 6652 1e-45 169
171
+ 369 gi|4558520|gb|AF033819.3| 98.00 100 2 0 1 100 7296 7395 2e-47 174
172
+ 370 gi|4558520|gb|AF033819.3| 96.00 100 3 1 3 102 30 128 2e-43 161
173
+ 370 gi|4558520|gb|AF033819.3| 95.59 68 2 1 3 70 9115 9181 2e-27 108
174
+ 371 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 6786 6687 4e-39 147
175
+ 372 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 5867 5768 4e-44 163
176
+ 376 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 5460 5559 4e-44 163
177
+ 377 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 1437 1536 2e-43 161
178
+ 380 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 3968 3869 3e-45 167
179
+ 385 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6936 7035 2e-42 158
180
+ 387 gi|4558520|gb|AF033819.3| 96.94 98 1 2 1 97 1860 1764 4e-44 163
181
+ 388 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7149 7248 2e-42 158
182
+ 389 gi|4558520|gb|AF033819.3| 97.94 97 2 0 1 97 6961 6865 1e-45 169
183
+ 393 gi|4558520|gb|AF033819.3| 94.06 101 5 1 1 101 677 776 1e-40 152
184
+ 396 gi|4558520|gb|AF033819.3| 95.00 100 3 2 1 98 2539 2440 7e-42 156
185
+ 404 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 5732 5633 7e-42 156
186
+ 405 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 5455 5554 2e-43 161
187
+ 407 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 6462 6561 2e-42 158
188
+ 408 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 220 121 2e-42 158
189
+ 412 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 4617 4518 1e-40 152
190
+ 413 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 3678 3777 2e-42 158
191
+ 416 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 8724 8625 1e-40 152
192
+ 417 gi|4558520|gb|AF033819.3| 93.00 100 7 0 1 100 6576 6675 4e-39 147
193
+ 418 gi|4558520|gb|AF033819.3| 95.88 97 3 1 1 96 8638 8542 7e-42 156
194
+ 420 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 8851 8752 2e-43 161
195
+ 421 gi|4558520|gb|AF033819.3| 93.07 101 6 1 1 101 2322 2223 5e-39 147
196
+ 422 gi|4558520|gb|AF033819.3| 93.00 100 6 1 1 99 6743 6644 2e-38 145
197
+ 425 gi|4558520|gb|AF033819.3| 92.00 100 7 1 1 99 3990 3891 7e-37 139
198
+ 426 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 3598 3697 1e-45 169
199
+ 428 gi|4558520|gb|AF033819.3| 96.04 101 4 0 1 101 1407 1507 1e-44 165
200
+ 429 gi|4558520|gb|AF033819.3| 97.00 100 1 2 1 98 3439 3340 3e-45 167
201
+ 436 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8315 8414 7e-42 156
202
+ 438 gi|4558520|gb|AF033819.3| 96.00 100 4 0 1 100 1808 1907 4e-44 163
203
+ 439 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7868 7769 1e-45 169
204
+ 440 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 7249 7348 1e-45 169
205
+ 441 gi|4558520|gb|AF033819.3| 93.94 99 6 0 1 99 5687 5589 3e-40 150
206
+ 443 gi|4558520|gb|AF033819.3| 98.02 101 1 1 1 101 8474 8573 2e-47 174
207
+ 446 gi|4558520|gb|AF033819.3| 95.96 99 4 0 1 99 2138 2236 2e-43 161
208
+ 448 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 4172 4073 2e-42 158
209
+ 450 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 100 5366 5268 7e-42 156
210
+ 451 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 7335 7236 2e-43 161
211
+ 454 gi|4558520|gb|AF033819.3| 94.06 101 4 2 1 101 2460 2558 1e-40 152
212
+ 455 gi|4558520|gb|AF033819.3| 95.05 101 4 1 1 101 1266 1167 2e-42 158
213
+ 457 gi|4558520|gb|AF033819.3| 95.88 97 3 1 1 97 3177 3082 7e-42 156
214
+ 463 gi|4558520|gb|AF033819.3| 99.00 100 1 0 1 100 5227 5128 4e-49 180
215
+ 464 gi|4558520|gb|AF033819.3| 96.84 95 3 0 1 95 8589 8683 6e-43 159
216
+ 465 gi|4558520|gb|AF033819.3| 93.20 103 4 3 1 103 2775 2676 1e-39 148
217
+ 466 gi|4558520|gb|AF033819.3| 95.00 100 4 1 1 99 8430 8331 7e-42 156
218
+ 470 gi|4558520|gb|AF033819.3| 96.04 101 3 1 1 101 7790 7691 4e-44 163
219
+ 471 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 149 50 2e-42 158
220
+ 472 gi|4558520|gb|AF033819.3| 98.00 100 1 1 1 99 1495 1396 7e-47 172
221
+ 475 gi|4558520|gb|AF033819.3| 94.00 100 6 0 1 100 140 41 1e-40 152
222
+ 476 gi|4558520|gb|AF033819.3| 96.00 100 3 1 1 99 2215 2116 2e-43 161
223
+ 482 gi|4558520|gb|AF033819.3| 93.94 99 3 3 1 96 5480 5578 4e-39 147
224
+ 485 gi|4558520|gb|AF033819.3| 95.00 100 5 0 1 100 7907 7808 2e-42 158
225
+ 486 gi|4558520|gb|AF033819.3| 94.00 100 3 3 1 98 4990 5088 1e-39 148
226
+ 487 gi|4558520|gb|AF033819.3| 97.00 100 2 1 1 99 9157 9058 3e-45 167
227
+ 487 gi|4558520|gb|AF033819.3| 95.83 72 2 1 1 71 72 1 1e-29 115
228
+ 488 gi|4558520|gb|AF033819.3| 95.10 102 2 3 1 101 231 132 2e-42 158
229
+ 490 gi|4558520|gb|AF033819.3| 95.10 102 3 2 1 102 7064 6965 6e-43 159
230
+ 492 gi|4558520|gb|AF033819.3| 96.84 95 2 1 1 94 6389 6295 2e-42 158
231
+ 495 gi|4558520|gb|AF033819.3| 97.00 100 3 0 1 100 4727 4826 1e-45 169
232
+ 498 gi|4558520|gb|AF033819.3| 96.08 102 2 1 1 102 4303 4204 1e-44 165
233
+ 499 gi|4558520|gb|AF033819.3| 98.00 100 1 1 1 99 6832 6931 7e-47 172
data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim ADDED
@@ -0,0 +1 @@
1
+ gi|4558520|gb|AF033819.3| 1 9182