partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (647) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +647 -129
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  633. test/paired/new-results/test.log +142 -133
  634. test/test.py +6 -0
  635. test/trees.nwk +100 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-alleles.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-germlines.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/compare-plotdirs.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/extract-pairing-info.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/gctree-run.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/get-naive-probabilities.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/parse-output.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/split-loci.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/WHEEL +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/entry_points.txt +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/licenses/COPYING +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/sw/hmms/IGHD2-21_star_02.yaml ADDED
@@ -0,0 +1,681 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.021739130434782608
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+ overall_mute_freq: 0.08956521739130437
5
+ per_gene_mute_freq: 0.1075949291878152
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+ name: IGHD2-21_star_02
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHD2-21_star_02_0: 0.017857142857142856
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+ IGHD2-21_star_02_1: 0.017857142857142856
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+ IGHD2-21_star_02_10: 0.017857142857142856
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+ IGHD2-21_star_02_11: 0.017857142857142856
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+ IGHD2-21_star_02_12: 0.017857142857142856
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+ IGHD2-21_star_02_13: 0.017857142857142856
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+ IGHD2-21_star_02_14: 0.017857142857142856
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+ IGHD2-21_star_02_15: 0.017857142857142856
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+ IGHD2-21_star_02_16: 0.017857142857142856
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+ IGHD2-21_star_02_17: 0.017857142857142856
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+ IGHD2-21_star_02_18: 0.017857142857142856
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+ IGHD2-21_star_02_19: 0.017857142857142856
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+ IGHD2-21_star_02_2: 0.017857142857142856
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+ IGHD2-21_star_02_20: 0.017857142857142856
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+ IGHD2-21_star_02_21: 0.017857142857142856
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+ IGHD2-21_star_02_22: 0.017857142857142856
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+ IGHD2-21_star_02_23: 0.017857142857142856
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+ IGHD2-21_star_02_24: 0.017857142857142856
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+ IGHD2-21_star_02_25: 0.017857142857142856
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+ IGHD2-21_star_02_26: 0.017857142857142856
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+ IGHD2-21_star_02_27: 0.017857142857142856
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+ IGHD2-21_star_02_3: 0.017857142857142856
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+ IGHD2-21_star_02_4: 0.017857142857142856
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+ IGHD2-21_star_02_5: 0.017857142857142856
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+ IGHD2-21_star_02_6: 0.017857142857142856
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+ IGHD2-21_star_02_7: 0.017857142857142856
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+ IGHD2-21_star_02_8: 0.017857142857142856
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+ IGHD2-21_star_02_9: 0.017857142857142856
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+ insert_left_A: 0.09854014598540146
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+ insert_left_C: 0.16970802919708028
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+ insert_left_G: 0.10948905109489052
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+ insert_left_T: 0.12226277372262774
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.8924050708121848
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+ C: 0.0358649763959384
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+ G: 0.0358649763959384
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+ T: 0.0358649763959384
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: A
57
+ name: insert_left_A
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+ transitions:
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+ IGHD2-21_star_02_0: 0.017857142857142856
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+ IGHD2-21_star_02_1: 0.017857142857142856
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+ IGHD2-21_star_02_10: 0.017857142857142856
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+ IGHD2-21_star_02_11: 0.017857142857142856
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+ IGHD2-21_star_02_12: 0.017857142857142856
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+ IGHD2-21_star_02_13: 0.017857142857142856
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+ IGHD2-21_star_02_14: 0.017857142857142856
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+ IGHD2-21_star_02_15: 0.017857142857142856
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+ IGHD2-21_star_02_16: 0.017857142857142856
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+ IGHD2-21_star_02_17: 0.017857142857142856
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+ IGHD2-21_star_02_18: 0.017857142857142856
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+ IGHD2-21_star_02_19: 0.017857142857142856
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+ IGHD2-21_star_02_2: 0.017857142857142856
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+ IGHD2-21_star_02_20: 0.017857142857142856
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+ IGHD2-21_star_02_21: 0.017857142857142856
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+ IGHD2-21_star_02_22: 0.017857142857142856
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+ IGHD2-21_star_02_23: 0.017857142857142856
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+ IGHD2-21_star_02_24: 0.017857142857142856
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+ IGHD2-21_star_02_25: 0.017857142857142856
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+ IGHD2-21_star_02_26: 0.017857142857142856
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+ IGHD2-21_star_02_27: 0.017857142857142856
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+ IGHD2-21_star_02_3: 0.017857142857142856
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+ IGHD2-21_star_02_4: 0.017857142857142856
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+ IGHD2-21_star_02_5: 0.017857142857142856
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+ IGHD2-21_star_02_6: 0.017857142857142856
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+ IGHD2-21_star_02_7: 0.017857142857142856
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+ IGHD2-21_star_02_8: 0.017857142857142856
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+ IGHD2-21_star_02_9: 0.017857142857142856
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+ insert_left_A: 0.09854014598540146
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+ insert_left_C: 0.16970802919708028
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+ insert_left_G: 0.10948905109489052
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+ insert_left_T: 0.12226277372262774
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.0358649763959384
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+ C: 0.8924050708121848
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+ G: 0.0358649763959384
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+ T: 0.0358649763959384
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: C
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+ name: insert_left_C
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+ transitions:
105
+ IGHD2-21_star_02_0: 0.017857142857142856
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+ IGHD2-21_star_02_1: 0.017857142857142856
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+ IGHD2-21_star_02_10: 0.017857142857142856
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+ IGHD2-21_star_02_11: 0.017857142857142856
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+ IGHD2-21_star_02_12: 0.017857142857142856
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+ IGHD2-21_star_02_13: 0.017857142857142856
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+ IGHD2-21_star_02_14: 0.017857142857142856
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+ IGHD2-21_star_02_15: 0.017857142857142856
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+ IGHD2-21_star_02_16: 0.017857142857142856
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+ IGHD2-21_star_02_17: 0.017857142857142856
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+ IGHD2-21_star_02_18: 0.017857142857142856
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+ IGHD2-21_star_02_19: 0.017857142857142856
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+ IGHD2-21_star_02_2: 0.017857142857142856
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+ IGHD2-21_star_02_20: 0.017857142857142856
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+ IGHD2-21_star_02_21: 0.017857142857142856
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+ IGHD2-21_star_02_22: 0.017857142857142856
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+ IGHD2-21_star_02_23: 0.017857142857142856
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+ IGHD2-21_star_02_24: 0.017857142857142856
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+ IGHD2-21_star_02_25: 0.017857142857142856
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+ IGHD2-21_star_02_26: 0.017857142857142856
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+ IGHD2-21_star_02_27: 0.017857142857142856
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+ IGHD2-21_star_02_3: 0.017857142857142856
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+ IGHD2-21_star_02_4: 0.017857142857142856
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+ IGHD2-21_star_02_5: 0.017857142857142856
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+ IGHD2-21_star_02_6: 0.017857142857142856
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+ IGHD2-21_star_02_7: 0.017857142857142856
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+ IGHD2-21_star_02_8: 0.017857142857142856
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+ IGHD2-21_star_02_9: 0.017857142857142856
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+ insert_left_A: 0.09854014598540146
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+ insert_left_C: 0.16970802919708028
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+ insert_left_G: 0.10948905109489052
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+ insert_left_T: 0.12226277372262774
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.0358649763959384
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+ G: 0.8924050708121848
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+ T: 0.0358649763959384
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: insert_left_G
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+ transitions:
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+ IGHD2-21_star_02_0: 0.017857142857142856
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+ IGHD2-21_star_02_1: 0.017857142857142856
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+ IGHD2-21_star_02_10: 0.017857142857142856
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+ IGHD2-21_star_02_11: 0.017857142857142856
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+ IGHD2-21_star_02_12: 0.017857142857142856
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+ IGHD2-21_star_02_13: 0.017857142857142856
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+ IGHD2-21_star_02_14: 0.017857142857142856
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+ IGHD2-21_star_02_15: 0.017857142857142856
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+ IGHD2-21_star_02_16: 0.017857142857142856
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+ IGHD2-21_star_02_17: 0.017857142857142856
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+ IGHD2-21_star_02_18: 0.017857142857142856
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+ IGHD2-21_star_02_19: 0.017857142857142856
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+ IGHD2-21_star_02_2: 0.017857142857142856
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+ IGHD2-21_star_02_20: 0.017857142857142856
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+ IGHD2-21_star_02_21: 0.017857142857142856
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+ IGHD2-21_star_02_22: 0.017857142857142856
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+ IGHD2-21_star_02_23: 0.017857142857142856
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+ IGHD2-21_star_02_24: 0.017857142857142856
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+ IGHD2-21_star_02_25: 0.017857142857142856
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+ IGHD2-21_star_02_26: 0.017857142857142856
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+ IGHD2-21_star_02_27: 0.017857142857142856
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+ IGHD2-21_star_02_3: 0.017857142857142856
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+ IGHD2-21_star_02_4: 0.017857142857142856
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+ IGHD2-21_star_02_5: 0.017857142857142856
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+ IGHD2-21_star_02_6: 0.017857142857142856
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+ IGHD2-21_star_02_7: 0.017857142857142856
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+ IGHD2-21_star_02_8: 0.017857142857142856
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+ IGHD2-21_star_02_9: 0.017857142857142856
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+ insert_left_A: 0.09854014598540146
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+ insert_left_C: 0.16970802919708028
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+ insert_left_G: 0.10948905109489052
182
+ insert_left_T: 0.12226277372262774
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ C: 0.0358649763959384
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+ T: 0.8924050708121848
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ germline: T
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+ name: insert_left_T
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+ transitions:
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+ IGHD2-21_star_02_0: 0.017857142857142856
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+ IGHD2-21_star_02_1: 0.017857142857142856
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+ IGHD2-21_star_02_10: 0.017857142857142856
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+ IGHD2-21_star_02_11: 0.017857142857142856
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+ IGHD2-21_star_02_12: 0.017857142857142856
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+ IGHD2-21_star_02_14: 0.017857142857142856
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+ IGHD2-21_star_02_18: 0.017857142857142856
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+ IGHD2-21_star_02_20: 0.017857142857142856
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+ IGHD2-21_star_02_22: 0.017857142857142856
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+ IGHD2-21_star_02_23: 0.017857142857142856
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+ IGHD2-21_star_02_24: 0.017857142857142856
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+ IGHD2-21_star_02_25: 0.017857142857142856
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+ IGHD2-21_star_02_26: 0.017857142857142856
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+ IGHD2-21_star_02_27: 0.017857142857142856
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+ IGHD2-21_star_02_3: 0.017857142857142856
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+ IGHD2-21_star_02_6: 0.017857142857142856
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+ IGHD2-21_star_02_7: 0.017857142857142856
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+ IGHD2-21_star_02_8: 0.017857142857142856
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+ IGHD2-21_star_02_9: 0.017857142857142856
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+ insert_left_C: 0.16970802919708028
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+ insert_left_G: 0.10948905109489052
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+ insert_left_T: 0.12226277372262774
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ name: IGHD2-21_star_02_0
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+ transitions:
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+ IGHD2-21_star_02_1: 0.9636363636363636
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+ end: 0.03636363636363636
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ transitions:
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+ end: 0.03636363636363636
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.03636363636363636
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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338
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+ end: 0.03636363636363636
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+ - !!python/object:python.hmmwriter.State
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+ G: 0.03587185532259167
379
+ T: 0.892384434032225
380
+ track: nukes
381
+ extras:
382
+ ambiguous_char: N
383
+ ambiguous_emission_prob: 0.25
384
+ germline: T
385
+ name: IGHD2-21_star_02_9
386
+ transitions:
387
+ IGHD2-21_star_02_10: 0.9636363636363636
388
+ end: 0.03636363636363636
389
+ - !!python/object:python.hmmwriter.State
390
+ emissions:
391
+ probs:
392
+ A: 0.03587185532259167
393
+ C: 0.03587185532259167
394
+ G: 0.892384434032225
395
+ T: 0.03587185532259167
396
+ track: nukes
397
+ extras:
398
+ ambiguous_char: N
399
+ ambiguous_emission_prob: 0.25
400
+ germline: G
401
+ name: IGHD2-21_star_02_10
402
+ transitions:
403
+ IGHD2-21_star_02_11: 0.9636363636363636
404
+ end: 0.03636363636363636
405
+ - !!python/object:python.hmmwriter.State
406
+ emissions:
407
+ probs:
408
+ A: 0.03587185532259167
409
+ C: 0.03587185532259167
410
+ G: 0.892384434032225
411
+ T: 0.03587185532259167
412
+ track: nukes
413
+ extras:
414
+ ambiguous_char: N
415
+ ambiguous_emission_prob: 0.25
416
+ germline: G
417
+ name: IGHD2-21_star_02_11
418
+ transitions:
419
+ IGHD2-21_star_02_12: 0.9636363636363636
420
+ end: 0.03636363636363636
421
+ - !!python/object:python.hmmwriter.State
422
+ emissions:
423
+ probs:
424
+ A: 0.03587185532259167
425
+ C: 0.03587185532259167
426
+ G: 0.03587185532259167
427
+ T: 0.892384434032225
428
+ track: nukes
429
+ extras:
430
+ ambiguous_char: N
431
+ ambiguous_emission_prob: 0.25
432
+ germline: T
433
+ name: IGHD2-21_star_02_12
434
+ transitions:
435
+ IGHD2-21_star_02_13: 0.9636363636363636
436
+ end: 0.03636363636363636
437
+ - !!python/object:python.hmmwriter.State
438
+ emissions:
439
+ probs:
440
+ A: 0.03587185532259167
441
+ C: 0.03587185532259167
442
+ G: 0.892384434032225
443
+ T: 0.03587185532259167
444
+ track: nukes
445
+ extras:
446
+ ambiguous_char: N
447
+ ambiguous_emission_prob: 0.25
448
+ germline: G
449
+ name: IGHD2-21_star_02_13
450
+ transitions:
451
+ IGHD2-21_star_02_14: 0.9636363636363636
452
+ end: 0.03636363636363636
453
+ - !!python/object:python.hmmwriter.State
454
+ emissions:
455
+ probs:
456
+ A: 0.03587185532259167
457
+ C: 0.03587185532259167
458
+ G: 0.892384434032225
459
+ T: 0.03587185532259167
460
+ track: nukes
461
+ extras:
462
+ ambiguous_char: N
463
+ ambiguous_emission_prob: 0.25
464
+ germline: G
465
+ name: IGHD2-21_star_02_14
466
+ transitions:
467
+ IGHD2-21_star_02_15: 0.9636363636363636
468
+ end: 0.03636363636363636
469
+ - !!python/object:python.hmmwriter.State
470
+ emissions:
471
+ probs:
472
+ A: 0.0375
473
+ C: 0.0375
474
+ G: 0.0375
475
+ T: 0.8875
476
+ track: nukes
477
+ extras:
478
+ ambiguous_char: N
479
+ ambiguous_emission_prob: 0.25
480
+ germline: T
481
+ name: IGHD2-21_star_02_15
482
+ transitions:
483
+ IGHD2-21_star_02_16: 0.9636363636363636
484
+ end: 0.03636363636363636
485
+ - !!python/object:python.hmmwriter.State
486
+ emissions:
487
+ probs:
488
+ A: 0.03587185532259167
489
+ C: 0.03587185532259167
490
+ G: 0.892384434032225
491
+ T: 0.03587185532259167
492
+ track: nukes
493
+ extras:
494
+ ambiguous_char: N
495
+ ambiguous_emission_prob: 0.25
496
+ germline: G
497
+ name: IGHD2-21_star_02_16
498
+ transitions:
499
+ IGHD2-21_star_02_17: 0.9636363636363636
500
+ end: 0.03636363636363636
501
+ - !!python/object:python.hmmwriter.State
502
+ emissions:
503
+ probs:
504
+ A: 0.892384434032225
505
+ C: 0.03587185532259167
506
+ G: 0.03587185532259167
507
+ T: 0.03587185532259167
508
+ track: nukes
509
+ extras:
510
+ ambiguous_char: N
511
+ ambiguous_emission_prob: 0.25
512
+ germline: A
513
+ name: IGHD2-21_star_02_17
514
+ transitions:
515
+ IGHD2-21_star_02_18: 0.9636363636363636
516
+ end: 0.03636363636363636
517
+ - !!python/object:python.hmmwriter.State
518
+ emissions:
519
+ probs:
520
+ A: 0.03587185532259167
521
+ C: 0.892384434032225
522
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523
+ T: 0.03587185532259167
524
+ track: nukes
525
+ extras:
526
+ ambiguous_char: N
527
+ ambiguous_emission_prob: 0.25
528
+ germline: C
529
+ name: IGHD2-21_star_02_18
530
+ transitions:
531
+ IGHD2-21_star_02_19: 0.9636363636363636
532
+ end: 0.03636363636363636
533
+ - !!python/object:python.hmmwriter.State
534
+ emissions:
535
+ probs:
536
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537
+ C: 0.03587109099740798
538
+ G: 0.03587109099740798
539
+ T: 0.8923867270077761
540
+ track: nukes
541
+ extras:
542
+ ambiguous_char: N
543
+ ambiguous_emission_prob: 0.25
544
+ germline: T
545
+ name: IGHD2-21_star_02_19
546
+ transitions:
547
+ IGHD2-21_star_02_20: 0.9636363636363636
548
+ end: 0.03636363636363636
549
+ - !!python/object:python.hmmwriter.State
550
+ emissions:
551
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552
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553
+ C: 0.03713666142131964
554
+ G: 0.8885900157360411
555
+ T: 0.03713666142131964
556
+ track: nukes
557
+ extras:
558
+ ambiguous_char: N
559
+ ambiguous_emission_prob: 0.25
560
+ germline: G
561
+ name: IGHD2-21_star_02_20
562
+ transitions:
563
+ IGHD2-21_star_02_21: 0.9636363636363636
564
+ end: 0.03636363636363636
565
+ - !!python/object:python.hmmwriter.State
566
+ emissions:
567
+ probs:
568
+ A: 0.035869562347040584
569
+ C: 0.8923913129588783
570
+ G: 0.035869562347040584
571
+ T: 0.035869562347040584
572
+ track: nukes
573
+ extras:
574
+ ambiguous_char: N
575
+ ambiguous_emission_prob: 0.25
576
+ germline: C
577
+ name: IGHD2-21_star_02_21
578
+ transitions:
579
+ IGHD2-21_star_02_22: 0.9636363636363636
580
+ end: 0.03636363636363636
581
+ - !!python/object:python.hmmwriter.State
582
+ emissions:
583
+ probs:
584
+ A: 0.035868798021856885
585
+ C: 0.035868798021856885
586
+ G: 0.035868798021856885
587
+ T: 0.8923936059344293
588
+ track: nukes
589
+ extras:
590
+ ambiguous_char: N
591
+ ambiguous_emission_prob: 0.25
592
+ germline: T
593
+ name: IGHD2-21_star_02_22
594
+ transitions:
595
+ IGHD2-21_star_02_23: 0.9636363636363636
596
+ end: 0.03636363636363636
597
+ - !!python/object:python.hmmwriter.State
598
+ emissions:
599
+ probs:
600
+ A: 0.8902250393401027
601
+ C: 0.0365916535532991
602
+ G: 0.0365916535532991
603
+ T: 0.0365916535532991
604
+ track: nukes
605
+ extras:
606
+ ambiguous_char: N
607
+ ambiguous_emission_prob: 0.25
608
+ germline: A
609
+ name: IGHD2-21_star_02_23
610
+ transitions:
611
+ IGHD2-21_star_02_24: 0.9636363636363636
612
+ end: 0.03636363636363636
613
+ - !!python/object:python.hmmwriter.State
614
+ emissions:
615
+ probs:
616
+ A: 0.035867269371489485
617
+ C: 0.035867269371489485
618
+ G: 0.035867269371489485
619
+ T: 0.8923981918855315
620
+ track: nukes
621
+ extras:
622
+ ambiguous_char: N
623
+ ambiguous_emission_prob: 0.25
624
+ germline: T
625
+ name: IGHD2-21_star_02_24
626
+ transitions:
627
+ IGHD2-21_star_02_25: 0.9818181818181818
628
+ end: 0.01818181818181818
629
+ - !!python/object:python.hmmwriter.State
630
+ emissions:
631
+ probs:
632
+ A: 0.035866505046305786
633
+ C: 0.035866505046305786
634
+ G: 0.035866505046305786
635
+ T: 0.8924004848610826
636
+ track: nukes
637
+ extras:
638
+ ambiguous_char: N
639
+ ambiguous_emission_prob: 0.25
640
+ germline: T
641
+ name: IGHD2-21_star_02_25
642
+ transitions:
643
+ IGHD2-21_star_02_26: 0.9636363636363636
644
+ end: 0.03636363636363636
645
+ - !!python/object:python.hmmwriter.State
646
+ emissions:
647
+ probs:
648
+ A: 0.035583682722315615
649
+ C: 0.8932489518330532
650
+ G: 0.035583682722315615
651
+ T: 0.035583682722315615
652
+ track: nukes
653
+ extras:
654
+ ambiguous_char: N
655
+ ambiguous_emission_prob: 0.25
656
+ germline: C
657
+ name: IGHD2-21_star_02_26
658
+ transitions:
659
+ IGHD2-21_star_02_27: 0.9636363636363636
660
+ end: 0.03636363636363636
661
+ - !!python/object:python.hmmwriter.State
662
+ emissions:
663
+ probs:
664
+ A: 0.0358649763959384
665
+ C: 0.8924050708121848
666
+ G: 0.0358649763959384
667
+ T: 0.0358649763959384
668
+ track: nukes
669
+ extras:
670
+ ambiguous_char: N
671
+ ambiguous_emission_prob: 0.25
672
+ germline: C
673
+ name: IGHD2-21_star_02_27
674
+ transitions:
675
+ end: 1.0
676
+ tracks:
677
+ nukes:
678
+ - A
679
+ - C
680
+ - G
681
+ - T