partis-bcr 1.0.8__py3-none-any.whl → 1.0.9.post1.dev1__py3-none-any.whl

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Files changed (156) hide show
  1. packages/ham/bcrham +0 -0
  2. packages/ig-sw/src/ig_align/ig-sw +0 -0
  3. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/METADATA +1 -1
  4. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/RECORD +155 -73
  5. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  6. test/new-results/test.log +12 -16
  7. test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv +8 -8
  8. test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -1
  9. test/paired/new-results/partition-new-simu/fasttree/iclust-0/log +8 -8
  10. test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -1
  11. test/paired/new-results/partition-new-simu/fasttree/iclust-1/log +7 -7
  12. test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -1
  13. test/paired/new-results/partition-new-simu/fasttree/iclust-2/log +9 -9
  14. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  15. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log +8 -8
  16. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out +1 -1
  17. test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log +9 -9
  18. test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml +1 -1
  19. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out +1 -1
  20. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log +8 -8
  21. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/fasttree.out +1 -1
  22. test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/log +4 -4
  23. test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml +1 -1
  24. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/fasttree.out +1 -1
  25. test/paired/new-results/partition-new-simu/igh+igl/partition-igh/fasttree/iclust-0/log +9 -9
  26. test/paired/new-results/partition-new-simu/igh+igl/partition-igh-selection-metrics.yaml +1 -1
  27. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/fasttree.out +1 -1
  28. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-0/log +9 -9
  29. test/paired/new-results/partition-new-simu/igh+igl/partition-igl/fasttree/iclust-1/log +3 -3
  30. test/paired/new-results/partition-new-simu/igh+igl/partition-igl-selection-metrics.yaml +1 -1
  31. test/paired/new-results/partition-new-simu/selection-metrics.yaml +1 -1
  32. test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml +1 -1
  33. test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg +107 -107
  34. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg +83 -83
  35. test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg +61 -61
  36. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg +18 -18
  37. test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg +24 -24
  38. test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg +35 -35
  39. test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg +22 -22
  40. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg +45 -45
  41. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg +45 -45
  42. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg +45 -45
  43. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg +15 -15
  44. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg +15 -15
  45. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg +47 -47
  46. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg +48 -48
  47. test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg +27 -27
  48. test/paired/new-results/run-times.csv +6 -6
  49. test/paired/new-results/subset-partition-new-simu/isub-0/partition.log +86 -102
  50. test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml +1 -1
  51. test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml +1 -1
  52. test/paired/new-results/subset-partition-new-simu/isub-1/partition.log +84 -100
  53. test/paired/new-results/subset-partition-new-simu/isub-1/single-chain/partition-igh.yaml +1 -1
  54. test/paired/new-results/subset-partition-new-simu/merged-partition.log +50 -54
  55. test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igh.yaml +1 -1
  56. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml +1 -1
  57. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml +1 -1
  58. test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml +1 -1
  59. test/paired/new-results/subset-partition-new-simu/merged-subsets/partition-igh.yaml +1 -1
  60. test/paired/new-results/test.log +203 -236
  61. test/ref-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  62. test/ref-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  63. test/ref-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  64. test/ref-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  65. test/ref-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  66. test/ref-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  67. test/ref-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  68. test/ref-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  69. test/ref-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  70. test/ref-results/partition-new-simu/iqtree/iclust-0/input-seqs.fa +24 -0
  71. test/ref-results/partition-new-simu/iqtree/iclust-0/log +430 -0
  72. test/ref-results/partition-new-simu/iqtree/iclust-0/out.bionj +1 -0
  73. test/ref-results/partition-new-simu/iqtree/iclust-0/out.ckp.gz +0 -0
  74. test/ref-results/partition-new-simu/iqtree/iclust-0/out.iqtree +282 -0
  75. test/ref-results/partition-new-simu/iqtree/iclust-0/out.log +429 -0
  76. test/ref-results/partition-new-simu/iqtree/iclust-0/out.mldist +13 -0
  77. test/ref-results/partition-new-simu/iqtree/iclust-0/out.model.gz +0 -0
  78. test/ref-results/partition-new-simu/iqtree/iclust-0/out.state +3529 -0
  79. test/ref-results/partition-new-simu/iqtree/iclust-0/out.treefile +1 -0
  80. test/ref-results/partition-new-simu/iqtree/iclust-1/input-seqs.fa +16 -0
  81. test/ref-results/partition-new-simu/iqtree/iclust-1/log +373 -0
  82. test/ref-results/partition-new-simu/iqtree/iclust-1/out.bionj +1 -0
  83. test/ref-results/partition-new-simu/iqtree/iclust-1/out.ckp.gz +0 -0
  84. test/ref-results/partition-new-simu/iqtree/iclust-1/out.iqtree +279 -0
  85. test/ref-results/partition-new-simu/iqtree/iclust-1/out.log +372 -0
  86. test/ref-results/partition-new-simu/iqtree/iclust-1/out.mldist +9 -0
  87. test/ref-results/partition-new-simu/iqtree/iclust-1/out.model.gz +0 -0
  88. test/ref-results/partition-new-simu/iqtree/iclust-1/out.state +2229 -0
  89. test/ref-results/partition-new-simu/iqtree/iclust-1/out.treefile +1 -0
  90. test/ref-results/partition-new-simu/iqtree/iclust-2/input-seqs.fa +16 -0
  91. test/ref-results/partition-new-simu/iqtree/iclust-2/log +375 -0
  92. test/ref-results/partition-new-simu/iqtree/iclust-2/out.bionj +1 -0
  93. test/ref-results/partition-new-simu/iqtree/iclust-2/out.ckp.gz +0 -0
  94. test/ref-results/partition-new-simu/iqtree/iclust-2/out.iqtree +274 -0
  95. test/ref-results/partition-new-simu/iqtree/iclust-2/out.log +374 -0
  96. test/ref-results/partition-new-simu/iqtree/iclust-2/out.mldist +9 -0
  97. test/ref-results/partition-new-simu/iqtree/iclust-2/out.model.gz +0 -0
  98. test/ref-results/partition-new-simu/iqtree/iclust-2/out.state +2283 -0
  99. test/ref-results/partition-new-simu/iqtree/iclust-2/out.treefile +1 -0
  100. test/ref-results/partition-new-simu/iqtree-annotations.yaml +1 -0
  101. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa +24 -0
  102. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralProbs +3461 -0
  103. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralStates +10 -0
  104. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.ancestralTree +1 -0
  105. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestModel +1 -0
  106. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTree +1 -0
  107. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  108. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.log +216 -0
  109. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.mlTrees +20 -0
  110. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.rba +0 -0
  111. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.reduced.phy +9 -0
  112. test/ref-results/partition-new-simu/raxml/iclust-0/input-seqs.fa.raxml.startTree +20 -0
  113. test/ref-results/partition-new-simu/raxml/iclust-0/log +454 -0
  114. test/ref-results/partition-new-simu/raxml/iclust-0/run.sh +3 -0
  115. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa +16 -0
  116. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralProbs +2203 -0
  117. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralStates +6 -0
  118. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.ancestralTree +1 -0
  119. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestModel +1 -0
  120. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTree +1 -0
  121. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  122. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.log +217 -0
  123. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.mlTrees +20 -0
  124. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.rba +0 -0
  125. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.reduced.phy +4 -0
  126. test/ref-results/partition-new-simu/raxml/iclust-1/input-seqs.fa.raxml.startTree +20 -0
  127. test/ref-results/partition-new-simu/raxml/iclust-1/log +440 -0
  128. test/ref-results/partition-new-simu/raxml/iclust-1/run.sh +3 -0
  129. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa +16 -0
  130. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralProbs +2275 -0
  131. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralStates +6 -0
  132. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.ancestralTree +1 -0
  133. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestModel +1 -0
  134. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTree +1 -0
  135. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.bestTreeCollapsed +1 -0
  136. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.log +207 -0
  137. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.mlTrees +20 -0
  138. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.rba +0 -0
  139. test/ref-results/partition-new-simu/raxml/iclust-2/input-seqs.fa.raxml.startTree +20 -0
  140. test/ref-results/partition-new-simu/raxml/iclust-2/log +420 -0
  141. test/ref-results/partition-new-simu/raxml/iclust-2/run.sh +3 -0
  142. test/ref-results/partition-new-simu/raxml-annotations.yaml +1 -0
  143. bin/FastTree-macos +0 -0
  144. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-alleles.py +0 -0
  145. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/cf-germlines.py +0 -0
  146. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/compare-plotdirs.py +0 -0
  147. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/extract-pairing-info.py +0 -0
  148. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/gctree-run.py +0 -0
  149. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/get-naive-probabilities.py +0 -0
  150. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/parse-output.py +0 -0
  151. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/partis-test.py +0 -0
  152. {partis_bcr-1.0.8.data → partis_bcr-1.0.9.post1.dev1.data}/scripts/split-loci.py +0 -0
  153. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/WHEEL +0 -0
  154. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/entry_points.txt +0 -0
  155. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/licenses/COPYING +0 -0
  156. {partis_bcr-1.0.8.dist-info → partis_bcr-1.0.9.post1.dev1.dist-info}/top_level.txt +0 -0
test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml CHANGED
@@ -1 +1 @@
1
- {"version-info": {"partis-yaml": 0.1, "partis-git": {"commit": "db1170373f90d7278246df030159db6b40d1b594", "tag": "v1.0.8"}}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ4*01": "TTTTGTATTTGGTGGAGGAACCCAGCTGATCATTTTAG", "IGLJ5*01": "CTGGGTGTTTGGTGAGGGGACCGAGCTGACCGTCCTAG", "IGLJ5*02": "CTGGGTGTTTGGTGAGGGGACGGAGCTGACCGTCCTAG", "IGLJ6*01": "TAATGTGTTCGGCAGTGGCACCAAGGTGACCGTCCTCG", "IGLJ7*01": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGTCCTCG", "IGLJ7*02": "TGCTGTGTTCGGAGGAGGCACCCAGCTGACCGCCCTCG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ5*02": 7, "IGLJ5*01": 7, "IGLJ6*01": 7, "IGLJ7*01": 7, "IGLJ7*02": 7, "IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ4*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 21, "n_procs": 1, "partition": [["253ca59333-igl"], ["b739ce37b7-igl"], ["aa25e6c0ce-igl"], ["7588f09c07-igl"], ["8807c8ff04-igl"], ["20909c3943-igl"], ["a3baa83300-igl"], ["971ac047ee-igl"], ["a2238f4e9a-igl"], ["8d79fca804-igl"], ["0eb272ee70-igl"], ["09f5010bd3-igl"], ["b02ee7754a-igl"], ["ddcf0ca433-igl"], ["eee6809ad6-igl"], ["14195e4958-igl"], ["d5ddf0c2ec-igl"], ["57537e5f22-igl"], ["b1e56e40a1-igl"], ["21cea6e4d0-igl"], ["4d37fe487e-igl"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["253ca59333-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mut_freqs": [0.014970059880239521], "n_mutations": [5], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": 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