partis-bcr 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

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 (104) hide show
  1. bin/FastTree +0 -0
  2. bin/add-chimeras.py +59 -0
  3. bin/add-seqs-to-outputs.py +81 -0
  4. bin/bcr-phylo-run.py +799 -0
  5. bin/build.sh +24 -0
  6. bin/cf-alleles.py +97 -0
  7. bin/cf-germlines.py +57 -0
  8. bin/cf-linearham.py +199 -0
  9. bin/chimera-plot.py +76 -0
  10. bin/choose-partially-paired.py +143 -0
  11. bin/circle-plots.py +30 -0
  12. bin/compare-plotdirs.py +298 -0
  13. bin/diff-parameters.py +133 -0
  14. bin/docker-hub-push.sh +6 -0
  15. bin/extract-pairing-info.py +55 -0
  16. bin/gcdyn-simu-run.py +223 -0
  17. bin/gctree-run.py +244 -0
  18. bin/get-naive-probabilities.py +126 -0
  19. bin/iqtree-1.6.12 +0 -0
  20. bin/lonr.r +1020 -0
  21. bin/makeHtml +52 -0
  22. bin/mds-run.py +46 -0
  23. bin/parse-output.py +277 -0
  24. bin/partis +1869 -0
  25. bin/partis-pip +116 -0
  26. bin/partis.py +1869 -0
  27. bin/plot-gl-set-trees.py +519 -0
  28. bin/plot-hmms.py +151 -0
  29. bin/plot-lb-tree.py +427 -0
  30. bin/raxml-ng +0 -0
  31. bin/read-bcr-phylo-trees.py +38 -0
  32. bin/read-gctree-output.py +166 -0
  33. bin/run-chimeras.sh +64 -0
  34. bin/run-dtr-scan.sh +25 -0
  35. bin/run-paired-loci.sh +100 -0
  36. bin/run-tree-metrics.sh +88 -0
  37. bin/smetric-run.py +62 -0
  38. bin/split-loci.py +317 -0
  39. bin/swarm-2.1.13-linux-x86_64 +0 -0
  40. bin/test-germline-inference.py +425 -0
  41. bin/tree-perf-run.py +194 -0
  42. bin/vsearch-2.4.3-linux-x86_64 +0 -0
  43. bin/vsearch-2.4.3-macos-x86_64 +0 -0
  44. bin/xvfb-run +194 -0
  45. partis_bcr-1.0.2.data/scripts/cf-alleles.py +97 -0
  46. partis_bcr-1.0.2.data/scripts/cf-germlines.py +57 -0
  47. partis_bcr-1.0.2.data/scripts/extract-pairing-info.py +55 -0
  48. partis_bcr-1.0.2.data/scripts/gctree-run.py +244 -0
  49. partis_bcr-1.0.2.data/scripts/parse-output.py +277 -0
  50. partis_bcr-1.0.2.data/scripts/split-loci.py +317 -0
  51. partis_bcr-1.0.2.data/scripts/test.py +1005 -0
  52. {partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/METADATA +1 -1
  53. {partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/RECORD +101 -51
  54. partis_bcr-1.0.2.dist-info/top_level.txt +1 -0
  55. {partis → python}/glutils.py +1 -1
  56. python/main.py +30 -0
  57. {partis → python}/plotting.py +10 -1
  58. {partis → python}/treeutils.py +18 -16
  59. {partis → python}/utils.py +14 -7
  60. packages/ham/bcrham +0 -0
  61. partis/main.py +0 -59
  62. partis_bcr-1.0.0.dist-info/top_level.txt +0 -1
  63. {partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/WHEEL +0 -0
  64. {partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/entry_points.txt +0 -0
  65. {partis_bcr-1.0.0.dist-info → partis_bcr-1.0.2.dist-info}/licenses/COPYING +0 -0
  66. {partis → python}/__init__.py +0 -0
  67. {partis → python}/alleleclusterer.py +0 -0
  68. {partis → python}/allelefinder.py +0 -0
  69. {partis → python}/alleleremover.py +0 -0
  70. {partis → python}/annotationclustering.py +0 -0
  71. {partis → python}/baseutils.py +0 -0
  72. {partis → python}/cache/__init__.py +0 -0
  73. {partis → python}/cache/cached_uncertainties.py +0 -0
  74. {partis → python}/clusterpath.py +0 -0
  75. {partis → python}/coar.py +0 -0
  76. {partis → python}/corrcounter.py +0 -0
  77. {partis → python}/datautils.py +0 -0
  78. {partis → python}/event.py +0 -0
  79. {partis → python}/fraction_uncertainty.py +0 -0
  80. {partis → python}/gex.py +0 -0
  81. {partis → python}/glomerator.py +0 -0
  82. {partis → python}/hist.py +0 -0
  83. {partis → python}/hmmwriter.py +0 -0
  84. {partis → python}/hutils.py +0 -0
  85. {partis → python}/indelutils.py +0 -0
  86. {partis → python}/lbplotting.py +0 -0
  87. {partis → python}/mds.py +0 -0
  88. {partis → python}/mutefreqer.py +0 -0
  89. {partis → python}/paircluster.py +0 -0
  90. {partis → python}/parametercounter.py +0 -0
  91. {partis → python}/paramutils.py +0 -0
  92. {partis → python}/partitiondriver.py +0 -0
  93. {partis → python}/partitionplotter.py +0 -0
  94. {partis → python}/performanceplotter.py +0 -0
  95. {partis → python}/plotconfig.py +0 -0
  96. {partis → python}/processargs.py +0 -0
  97. {partis → python}/prutils.py +0 -0
  98. {partis → python}/recombinator.py +0 -0
  99. {partis → python}/scanplot.py +0 -0
  100. {partis → python}/seqfileopener.py +0 -0
  101. {partis → python}/treegenerator.py +0 -0
  102. {partis → python}/viterbicluster.py +0 -0
  103. {partis → python}/vrc01.py +0 -0
  104. {partis → python}/waterer.py +0 -0
{partis → python}/vrc01.py RENAMED
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{partis → python}/waterer.py RENAMED
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