miga-base 1.2.17.0 → 1.2.17.2

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Files changed (265) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/version.rb +2 -2
  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 +165 -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 +356 -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/README.md +42 -0
  35. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  36. data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
  37. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  38. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  39. data/utils/enveomics/Scripts/BedGraph.tad.rb +138 -0
  40. data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
  41. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  42. data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
  43. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  44. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  45. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
  46. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  47. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  48. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  49. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  50. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  51. data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
  52. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  53. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  54. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  55. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  56. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  57. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  58. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
  59. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  60. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  61. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  62. data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
  63. data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
  64. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  65. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  66. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  67. data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
  68. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  69. data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
  70. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  71. data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
  72. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  73. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  74. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  75. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  76. data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
  77. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  78. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  79. data/utils/enveomics/Scripts/FastA.split.rb +79 -0
  80. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  81. data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
  82. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  83. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  84. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  85. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  86. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  87. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  88. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  89. data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
  90. data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
  91. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  92. data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
  93. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  94. data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
  95. data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
  96. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  97. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  98. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
  99. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  100. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  101. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  102. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  103. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  104. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  105. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  106. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
  107. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  108. data/utils/enveomics/Scripts/SRA.download.bash +67 -0
  109. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  110. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  111. data/utils/enveomics/Scripts/Table.barplot.R +31 -0
  112. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  113. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  114. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  115. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  116. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  117. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  118. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  119. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  120. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  121. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  122. data/utils/enveomics/Scripts/aai.rb +421 -0
  123. data/utils/enveomics/Scripts/ani.rb +362 -0
  124. data/utils/enveomics/Scripts/anir.rb +137 -0
  125. data/utils/enveomics/Scripts/clust.rand.rb +102 -0
  126. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  127. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  128. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  129. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  130. data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
  131. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  132. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  133. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
  134. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  135. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  136. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  137. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
  138. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  139. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  140. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  141. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  142. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  143. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  144. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  145. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
  146. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  147. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  148. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  149. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  150. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  151. data/utils/enveomics/Scripts/ogs.rb +104 -0
  152. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  153. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  154. data/utils/enveomics/Scripts/rbm.rb +108 -0
  155. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  156. data/utils/enveomics/Tests/Makefile +10 -0
  157. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  158. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  159. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  160. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  161. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  162. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  163. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  164. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  165. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  166. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  167. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  168. data/utils/enveomics/Tests/alkB.nwk +1 -0
  169. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  170. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  171. data/utils/enveomics/Tests/hiv1.faa +59 -0
  172. data/utils/enveomics/Tests/hiv1.fna +134 -0
  173. data/utils/enveomics/Tests/hiv2.faa +70 -0
  174. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  175. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  176. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  177. data/utils/enveomics/Tests/low-cov.bg.gz +0 -0
  178. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  179. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  180. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  181. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  182. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  183. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  184. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  185. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  186. data/utils/enveomics/build_enveomics_r.bash +45 -0
  187. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  188. data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
  189. data/utils/enveomics/enveomics.R/R/autoprune.R +167 -0
  190. data/utils/enveomics/enveomics.R/R/barplot.R +203 -0
  191. data/utils/enveomics/enveomics.R/R/cliopts.R +141 -0
  192. data/utils/enveomics/enveomics.R/R/df2dist.R +192 -0
  193. data/utils/enveomics/enveomics.R/R/growthcurve.R +349 -0
  194. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  195. data/utils/enveomics/enveomics.R/R/recplot.R +419 -0
  196. data/utils/enveomics/enveomics.R/R/recplot2.R +1698 -0
  197. data/utils/enveomics/enveomics.R/R/tribs.R +638 -0
  198. data/utils/enveomics/enveomics.R/R/utils.R +90 -0
  199. data/utils/enveomics/enveomics.R/README.md +81 -0
  200. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  201. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  202. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
  203. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
  204. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
  205. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
  206. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +47 -0
  207. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
  208. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
  209. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +26 -0
  210. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +26 -0
  211. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +44 -0
  212. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +111 -0
  213. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
  214. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +34 -0
  215. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +25 -0
  216. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +59 -0
  217. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +63 -0
  218. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +46 -0
  219. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +78 -0
  220. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
  221. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
  222. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +147 -0
  223. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
  224. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +27 -0
  225. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
  226. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +28 -0
  227. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +24 -0
  228. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +22 -0
  229. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +22 -0
  230. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +52 -0
  231. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
  232. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +21 -0
  233. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
  234. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +34 -0
  235. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +23 -0
  236. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +24 -0
  237. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +31 -0
  238. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +56 -0
  239. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +20 -0
  240. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
  241. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
  242. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
  243. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
  244. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
  245. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
  246. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
  247. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
  248. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
  249. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
  250. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  251. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  252. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +81 -0
  253. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +49 -0
  254. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +48 -0
  255. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
  256. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +22 -0
  257. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +22 -0
  258. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +22 -0
  259. data/utils/enveomics/globals.mk +8 -0
  260. data/utils/enveomics/manifest.json +9 -0
  261. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  262. data/utils/multitrim/README.md +67 -0
  263. data/utils/multitrim/multitrim.py +1555 -0
  264. data/utils/multitrim/multitrim.yml +13 -0
  265. metadata +268 -6

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