miga-base 0.4.3.0 → 0.5.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (120) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +1 -1
  3. data/lib/miga/cli.rb +43 -223
  4. data/lib/miga/cli/action/add.rb +91 -62
  5. data/lib/miga/cli/action/classify_wf.rb +97 -0
  6. data/lib/miga/cli/action/daemon.rb +14 -10
  7. data/lib/miga/cli/action/derep_wf.rb +95 -0
  8. data/lib/miga/cli/action/doctor.rb +83 -55
  9. data/lib/miga/cli/action/get.rb +68 -52
  10. data/lib/miga/cli/action/get_db.rb +206 -0
  11. data/lib/miga/cli/action/index_wf.rb +31 -0
  12. data/lib/miga/cli/action/init.rb +115 -190
  13. data/lib/miga/cli/action/init/daemon_helper.rb +124 -0
  14. data/lib/miga/cli/action/ls.rb +20 -11
  15. data/lib/miga/cli/action/ncbi_get.rb +199 -157
  16. data/lib/miga/cli/action/preproc_wf.rb +46 -0
  17. data/lib/miga/cli/action/quality_wf.rb +45 -0
  18. data/lib/miga/cli/action/stats.rb +147 -99
  19. data/lib/miga/cli/action/summary.rb +10 -4
  20. data/lib/miga/cli/action/tax_dist.rb +61 -46
  21. data/lib/miga/cli/action/tax_test.rb +46 -39
  22. data/lib/miga/cli/action/wf.rb +178 -0
  23. data/lib/miga/cli/base.rb +11 -0
  24. data/lib/miga/cli/objects_helper.rb +88 -0
  25. data/lib/miga/cli/opt_helper.rb +160 -0
  26. data/lib/miga/daemon.rb +7 -4
  27. data/lib/miga/dataset/base.rb +5 -5
  28. data/lib/miga/project/base.rb +4 -4
  29. data/lib/miga/project/result.rb +2 -1
  30. data/lib/miga/remote_dataset/base.rb +5 -5
  31. data/lib/miga/remote_dataset/download.rb +1 -1
  32. data/lib/miga/version.rb +3 -3
  33. data/scripts/cds.bash +3 -1
  34. data/scripts/essential_genes.bash +1 -0
  35. data/scripts/stats.bash +1 -1
  36. data/scripts/trimmed_fasta.bash +5 -3
  37. data/utils/distance/runner.rb +3 -0
  38. data/utils/distance/temporal.rb +10 -1
  39. data/utils/enveomics/Manifest/Tasks/fasta.json +5 -0
  40. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +7 -0
  41. data/utils/enveomics/Scripts/BlastTab.addlen.rb +33 -31
  42. data/utils/enveomics/Scripts/FastA.tag.rb +42 -41
  43. data/utils/enveomics/Scripts/HMM.essential.rb +85 -55
  44. data/utils/enveomics/Scripts/HMM.haai.rb +29 -20
  45. data/utils/enveomics/Scripts/SRA.download.bash +1 -1
  46. data/utils/enveomics/Scripts/aai.rb +163 -128
  47. data/utils/enveomics/build_enveomics_r.bash +11 -10
  48. data/utils/enveomics/enveomics.R/DESCRIPTION +3 -2
  49. data/utils/enveomics/enveomics.R/R/autoprune.R +141 -107
  50. data/utils/enveomics/enveomics.R/R/barplot.R +105 -86
  51. data/utils/enveomics/enveomics.R/R/cliopts.R +131 -115
  52. data/utils/enveomics/enveomics.R/R/df2dist.R +144 -106
  53. data/utils/enveomics/enveomics.R/R/growthcurve.R +201 -133
  54. data/utils/enveomics/enveomics.R/R/recplot.R +350 -315
  55. data/utils/enveomics/enveomics.R/R/recplot2.R +1334 -914
  56. data/utils/enveomics/enveomics.R/R/tribs.R +521 -361
  57. data/utils/enveomics/enveomics.R/R/utils.R +31 -15
  58. data/utils/enveomics/enveomics.R/README.md +7 -0
  59. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +17 -0
  60. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +17 -0
  61. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +17 -0
  62. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +16 -21
  63. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +31 -28
  64. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -19
  65. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +36 -26
  66. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -24
  67. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -24
  68. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +32 -33
  69. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +91 -64
  70. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +57 -37
  71. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -19
  72. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -18
  73. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +39 -26
  74. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +38 -25
  75. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +40 -26
  76. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +67 -49
  77. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +37 -28
  78. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +122 -97
  79. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +35 -31
  80. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -23
  81. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +68 -51
  82. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -24
  83. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -22
  84. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -20
  85. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -18
  86. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +41 -32
  87. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -24
  88. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -18
  89. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +40 -34
  90. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -24
  91. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -20
  92. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -20
  93. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -29
  94. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +41 -42
  95. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -18
  96. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +43 -33
  97. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +36 -28
  98. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +74 -56
  99. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +44 -31
  100. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -22
  101. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +32 -26
  102. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +59 -44
  103. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -21
  104. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -22
  105. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +63 -43
  106. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +38 -29
  107. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +38 -30
  108. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +111 -83
  109. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -18
  110. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -18
  111. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -18
  112. data/utils/find-medoid.R +3 -2
  113. data/utils/representatives.rb +5 -3
  114. data/utils/subclade/pipeline.rb +22 -11
  115. data/utils/subclade/runner.rb +5 -1
  116. data/utils/subclades-compile.rb +1 -1
  117. data/utils/subclades.R +9 -3
  118. metadata +15 -4
  119. data/utils/enveomics/enveomics.R/man/enveomics.R-package.Rd +0 -15
  120. data/utils/enveomics/enveomics.R/man/z$-methods.Rd +0 -26
data/utils/enveomics/enveomics.R/man/enveomics.R-package.Rd DELETED
@@ -1,15 +0,0 @@
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- \name{enveomics.R-package}
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- \alias{enveomics.R-package}
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- \alias{enveomics.R}
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- \docType{package}
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- \title{Various Utilities for Microbial Genomics and Metagenomics}
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- \description{A collection of functions for microbial ecology and other
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- applications of genomics and metagenomics. Companion package for the
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- Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
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- <DOI:10.7287/peerj.preprints.1900v1>).}
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- \author{Luis M. Rodriguez-R <lmrodriguezr@gmail.com> [aut, cre]}
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-
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- \keyword{ package }
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-
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-
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-
data/utils/enveomics/enveomics.R/man/z$-methods.Rd DELETED
@@ -1,26 +0,0 @@
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- \name{$-methods}
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- \docType{methods}
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- \alias{$-methods}
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- \alias{$,enve.GrowthCurve-method}
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- \alias{$,enve.RecPlot2-method}
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- \alias{$,enve.RecPlot2.Peak-method}
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- \title{ ~~ Methods for Function \code{$} ~~}
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- \description{
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- ~~ Methods for function \code{$} ~~
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- }
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- \section{Methods}{
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- \describe{
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-
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- \item{\code{signature(x = "enve.GrowthCurve")}}{
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- enve.GrowthCurve, a growth curve
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- }
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-
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- \item{\code{signature(x = "enve.RecPlot2")}}{
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- enve.RecPlot2, a recruitment plot
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- }
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-
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- \item{\code{signature(x = "enve.RecPlot2.Peak")}}{
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- enve.RecPlot2.Peak, a peak from a recruitment plot
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- }
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- }}
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- \keyword{methods}