partis-bcr 1.0.11__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.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 (655) 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.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +655 -128
  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
  197. test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
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  635. test/paired/new-results/test/simu/igh+igk/igk.yaml +1 -0
  636. test/paired/new-results/test/simu/igh+igl/igh.yaml +1 -0
  637. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/igh.yaml +1 -0
  639. test/paired/new-results/test/simu/igk.yaml +1 -0
  640. test/paired/new-results/test/simu/igl.yaml +1 -0
  641. test/paired/new-results/test/simu/meta.yaml +1 -0
  642. test/paired/new-results/test.log +225 -40
  643. test/test.py +6 -0
  644. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  645. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  646. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  647. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  648. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  649. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  650. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  651. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  652. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  653. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  654. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  655. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHJ4_star_02.yaml ADDED
@@ -0,0 +1,906 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.5434782608695652
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.07747781244701783
6
+ name: IGHJ4_star_02
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHJ4_star_02_0: 0.0005918910920390648
14
+ IGHJ4_star_02_1: 0.0005918910920390648
15
+ IGHJ4_star_02_10: 0.0005918910920390648
16
+ IGHJ4_star_02_11: 0.0005918910920390648
17
+ IGHJ4_star_02_12: 0.0011837821840781297
18
+ IGHJ4_star_02_13: 0.0005918910920390648
19
+ IGHJ4_star_02_14: 0.0005918910920390648
20
+ IGHJ4_star_02_2: 0.0005918910920390648
21
+ IGHJ4_star_02_3: 0.0017756732761171944
22
+ IGHJ4_star_02_4: 0.0029594554601953243
23
+ IGHJ4_star_02_5: 0.0005918910920390648
24
+ IGHJ4_star_02_6: 0.0011837821840781297
25
+ IGHJ4_star_02_7: 0.0017756732761171944
26
+ IGHJ4_star_02_8: 0.0029594554601953243
27
+ IGHJ4_star_02_9: 0.0017756732761171944
28
+ insert_left_A: 0.1976479280832461
29
+ insert_left_C: 0.30635428852903146
30
+ insert_left_G: 0.227295117295733
31
+ insert_left_T: 0.25035404223877844
32
+ - !!python/object:python.hmmwriter.State
33
+ emissions:
34
+ probs:
35
+ A: 0.9225221875529822
36
+ C: 0.025825937482339276
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+ G: 0.025825937482339276
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+ T: 0.025825937482339276
39
+ track: nukes
40
+ extras:
41
+ ambiguous_char: N
42
+ ambiguous_emission_prob: 0.25
43
+ germline: A
44
+ name: insert_left_A
45
+ transitions:
46
+ IGHJ4_star_02_0: 0.00188532387788636
47
+ IGHJ4_star_02_1: 0.00188532387788636
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+ IGHJ4_star_02_10: 0.00188532387788636
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+ IGHJ4_star_02_11: 0.00188532387788636
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+ IGHJ4_star_02_12: 0.00377064775577272
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+ IGHJ4_star_02_13: 0.00188532387788636
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+ IGHJ4_star_02_14: 0.00188532387788636
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+ IGHJ4_star_02_2: 0.00188532387788636
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+ IGHJ4_star_02_3: 0.00565597163365908
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+ IGHJ4_star_02_4: 0.0094266193894318
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+ IGHJ4_star_02_5: 0.00188532387788636
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+ IGHJ4_star_02_6: 0.00377064775577272
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+ IGHJ4_star_02_7: 0.00565597163365908
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+ IGHJ4_star_02_8: 0.0094266193894318
60
+ IGHJ4_star_02_9: 0.00565597163365908
61
+ insert_left_A: 0.1895748241178905
62
+ insert_left_C: 0.2938409773827303
63
+ insert_left_G: 0.2180110477355741
64
+ insert_left_T: 0.24012811054932798
65
+ - !!python/object:python.hmmwriter.State
66
+ emissions:
67
+ probs:
68
+ A: 0.025825937482339276
69
+ C: 0.9225221875529822
70
+ G: 0.025825937482339276
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+ T: 0.025825937482339276
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
75
+ ambiguous_emission_prob: 0.25
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+ germline: C
77
+ name: insert_left_C
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+ transitions:
79
+ IGHJ4_star_02_0: 0.00188532387788636
80
+ IGHJ4_star_02_1: 0.00188532387788636
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+ IGHJ4_star_02_10: 0.00188532387788636
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+ IGHJ4_star_02_11: 0.00188532387788636
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+ IGHJ4_star_02_12: 0.00377064775577272
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+ IGHJ4_star_02_13: 0.00188532387788636
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+ IGHJ4_star_02_14: 0.00188532387788636
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+ IGHJ4_star_02_2: 0.00188532387788636
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+ IGHJ4_star_02_3: 0.00565597163365908
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+ IGHJ4_star_02_4: 0.0094266193894318
89
+ IGHJ4_star_02_5: 0.00188532387788636
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+ IGHJ4_star_02_6: 0.00377064775577272
91
+ IGHJ4_star_02_7: 0.00565597163365908
92
+ IGHJ4_star_02_8: 0.0094266193894318
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+ IGHJ4_star_02_9: 0.00565597163365908
94
+ insert_left_A: 0.1895748241178905
95
+ insert_left_C: 0.2938409773827303
96
+ insert_left_G: 0.2180110477355741
97
+ insert_left_T: 0.24012811054932798
98
+ - !!python/object:python.hmmwriter.State
99
+ emissions:
100
+ probs:
101
+ A: 0.025825937482339276
102
+ C: 0.025825937482339276
103
+ G: 0.9225221875529822
104
+ T: 0.025825937482339276
105
+ track: nukes
106
+ extras:
107
+ ambiguous_char: N
108
+ ambiguous_emission_prob: 0.25
109
+ germline: G
110
+ name: insert_left_G
111
+ transitions:
112
+ IGHJ4_star_02_0: 0.00188532387788636
113
+ IGHJ4_star_02_1: 0.00188532387788636
114
+ IGHJ4_star_02_10: 0.00188532387788636
115
+ IGHJ4_star_02_11: 0.00188532387788636
116
+ IGHJ4_star_02_12: 0.00377064775577272
117
+ IGHJ4_star_02_13: 0.00188532387788636
118
+ IGHJ4_star_02_14: 0.00188532387788636
119
+ IGHJ4_star_02_2: 0.00188532387788636
120
+ IGHJ4_star_02_3: 0.00565597163365908
121
+ IGHJ4_star_02_4: 0.0094266193894318
122
+ IGHJ4_star_02_5: 0.00188532387788636
123
+ IGHJ4_star_02_6: 0.00377064775577272
124
+ IGHJ4_star_02_7: 0.00565597163365908
125
+ IGHJ4_star_02_8: 0.0094266193894318
126
+ IGHJ4_star_02_9: 0.00565597163365908
127
+ insert_left_A: 0.1895748241178905
128
+ insert_left_C: 0.2938409773827303
129
+ insert_left_G: 0.2180110477355741
130
+ insert_left_T: 0.24012811054932798
131
+ - !!python/object:python.hmmwriter.State
132
+ emissions:
133
+ probs:
134
+ A: 0.025825937482339276
135
+ C: 0.025825937482339276
136
+ G: 0.025825937482339276
137
+ T: 0.9225221875529822
138
+ track: nukes
139
+ extras:
140
+ ambiguous_char: N
141
+ ambiguous_emission_prob: 0.25
142
+ germline: T
143
+ name: insert_left_T
144
+ transitions:
145
+ IGHJ4_star_02_0: 0.00188532387788636
146
+ IGHJ4_star_02_1: 0.00188532387788636
147
+ IGHJ4_star_02_10: 0.00188532387788636
148
+ IGHJ4_star_02_11: 0.00188532387788636
149
+ IGHJ4_star_02_12: 0.00377064775577272
150
+ IGHJ4_star_02_13: 0.00188532387788636
151
+ IGHJ4_star_02_14: 0.00188532387788636
152
+ IGHJ4_star_02_2: 0.00188532387788636
153
+ IGHJ4_star_02_3: 0.00565597163365908
154
+ IGHJ4_star_02_4: 0.0094266193894318
155
+ IGHJ4_star_02_5: 0.00188532387788636
156
+ IGHJ4_star_02_6: 0.00377064775577272
157
+ IGHJ4_star_02_7: 0.00565597163365908
158
+ IGHJ4_star_02_8: 0.0094266193894318
159
+ IGHJ4_star_02_9: 0.00565597163365908
160
+ insert_left_A: 0.1895748241178905
161
+ insert_left_C: 0.2938409773827303
162
+ insert_left_G: 0.2180110477355741
163
+ insert_left_T: 0.24012811054932798
164
+ - !!python/object:python.hmmwriter.State
165
+ emissions:
166
+ probs:
167
+ A: 0.9225221875529822
168
+ C: 0.025825937482339276
169
+ G: 0.025825937482339276
170
+ T: 0.025825937482339276
171
+ track: nukes
172
+ extras:
173
+ ambiguous_char: N
174
+ ambiguous_emission_prob: 0.25
175
+ germline: A
176
+ name: IGHJ4_star_02_0
177
+ transitions:
178
+ IGHJ4_star_02_1: 1.0
179
+ - !!python/object:python.hmmwriter.State
180
+ emissions:
181
+ probs:
182
+ A: 0.02643605891698148
183
+ C: 0.9206918232490555
184
+ G: 0.02643605891698148
185
+ T: 0.02643605891698148
186
+ track: nukes
187
+ extras:
188
+ ambiguous_char: N
189
+ ambiguous_emission_prob: 0.25
190
+ germline: C
191
+ name: IGHJ4_star_02_1
192
+ transitions:
193
+ IGHJ4_star_02_2: 1.0
194
+ - !!python/object:python.hmmwriter.State
195
+ emissions:
196
+ probs:
197
+ A: 0.02712767232224868
198
+ C: 0.02712767232224868
199
+ G: 0.02712767232224868
200
+ T: 0.918616983033254
201
+ track: nukes
202
+ extras:
203
+ ambiguous_char: N
204
+ ambiguous_emission_prob: 0.25
205
+ germline: T
206
+ name: IGHJ4_star_02_2
207
+ transitions:
208
+ IGHJ4_star_02_3: 1.0
209
+ - !!python/object:python.hmmwriter.State
210
+ emissions:
211
+ probs:
212
+ A: 0.9138938594200349
213
+ C: 0.028702046859988384
214
+ G: 0.028702046859988384
215
+ T: 0.028702046859988384
216
+ track: nukes
217
+ extras:
218
+ ambiguous_char: N
219
+ ambiguous_emission_prob: 0.25
220
+ germline: A
221
+ name: IGHJ4_star_02_3
222
+ transitions:
223
+ IGHJ4_star_02_4: 1.0
224
+ - !!python/object:python.hmmwriter.State
225
+ emissions:
226
+ probs:
227
+ A: 0.027994083319204756
228
+ C: 0.9160177500423857
229
+ G: 0.027994083319204756
230
+ T: 0.027994083319204756
231
+ track: nukes
232
+ extras:
233
+ ambiguous_char: N
234
+ ambiguous_emission_prob: 0.25
235
+ germline: C
236
+ name: IGHJ4_star_02_4
237
+ transitions:
238
+ IGHJ4_star_02_5: 1.0
239
+ - !!python/object:python.hmmwriter.State
240
+ emissions:
241
+ probs:
242
+ A: 0.02798643886580654
243
+ C: 0.02798643886580654
244
+ G: 0.02798643886580654
245
+ T: 0.9160406834025804
246
+ track: nukes
247
+ extras:
248
+ ambiguous_char: N
249
+ ambiguous_emission_prob: 0.25
250
+ germline: T
251
+ name: IGHJ4_star_02_5
252
+ transitions:
253
+ IGHJ4_star_02_6: 1.0
254
+ - !!python/object:python.hmmwriter.State
255
+ emissions:
256
+ probs:
257
+ A: 0.027578156237637493
258
+ C: 0.027578156237637493
259
+ G: 0.027578156237637493
260
+ T: 0.9172655312870875
261
+ track: nukes
262
+ extras:
263
+ ambiguous_char: N
264
+ ambiguous_emission_prob: 0.25
265
+ germline: T
266
+ name: IGHJ4_star_02_6
267
+ transitions:
268
+ IGHJ4_star_02_7: 1.0
269
+ - !!python/object:python.hmmwriter.State
270
+ emissions:
271
+ probs:
272
+ A: 0.02645253887393053
273
+ C: 0.02645253887393053
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+ G: 0.02645253887393053
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+ T: 0.9206423833782084
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+ track: nukes
277
+ extras:
278
+ ambiguous_char: N
279
+ ambiguous_emission_prob: 0.25
280
+ germline: T
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+ name: IGHJ4_star_02_7
282
+ transitions:
283
+ IGHJ4_star_02_8: 1.0
284
+ - !!python/object:python.hmmwriter.State
285
+ emissions:
286
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+ A: 0.02351907050748023
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+ track: nukes
292
+ extras:
293
+ ambiguous_char: N
294
+ ambiguous_emission_prob: 0.25
295
+ germline: G
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+ name: IGHJ4_star_02_8
297
+ transitions:
298
+ IGHJ4_star_02_9: 1.0
299
+ - !!python/object:python.hmmwriter.State
300
+ emissions:
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+ A: 0.8426372031541403
303
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+ G: 0.06294511873834392
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+ T: 0.06294511873834392
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
309
+ ambiguous_emission_prob: 0.25
310
+ germline: A
311
+ name: IGHJ4_star_02_9
312
+ transitions:
313
+ IGHJ4_star_02_10: 1.0
314
+ - !!python/object:python.hmmwriter.State
315
+ emissions:
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317
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+ T: 0.02124630207450297
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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: IGHJ4_star_02_10
327
+ transitions:
328
+ IGHJ4_star_02_11: 1.0
329
+ - !!python/object:python.hmmwriter.State
330
+ emissions:
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334
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338
+ ambiguous_char: N
339
+ ambiguous_emission_prob: 0.25
340
+ germline: T
341
+ name: IGHJ4_star_02_11
342
+ transitions:
343
+ IGHJ4_star_02_12: 1.0
344
+ - !!python/object:python.hmmwriter.State
345
+ emissions:
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349
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353
+ ambiguous_char: N
354
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355
+ germline: A
356
+ name: IGHJ4_star_02_12
357
+ transitions:
358
+ IGHJ4_star_02_13: 1.0
359
+ - !!python/object:python.hmmwriter.State
360
+ emissions:
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+ track: nukes
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+ extras:
368
+ ambiguous_char: N
369
+ ambiguous_emission_prob: 0.25
370
+ germline: C
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+ name: IGHJ4_star_02_13
372
+ transitions:
373
+ IGHJ4_star_02_14: 1.0
374
+ - !!python/object:python.hmmwriter.State
375
+ emissions:
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+ track: nukes
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+ ambiguous_char: N
384
+ ambiguous_emission_prob: 0.25
385
+ germline: T
386
+ name: IGHJ4_star_02_14
387
+ transitions:
388
+ IGHJ4_star_02_15: 1.0
389
+ - !!python/object:python.hmmwriter.State
390
+ emissions:
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398
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399
+ ambiguous_emission_prob: 0.25
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+ germline: G
401
+ name: IGHJ4_star_02_15
402
+ transitions:
403
+ IGHJ4_star_02_16: 1.0
404
+ - !!python/object:python.hmmwriter.State
405
+ emissions:
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415
+ germline: G
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+ name: IGHJ4_star_02_16
417
+ transitions:
418
+ IGHJ4_star_02_17: 1.0
419
+ - !!python/object:python.hmmwriter.State
420
+ emissions:
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+ extras:
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+ germline: G
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+ name: IGHJ4_star_02_17
432
+ transitions:
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+ IGHJ4_star_02_18: 1.0
434
+ - !!python/object:python.hmmwriter.State
435
+ emissions:
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444
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445
+ germline: G
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+ name: IGHJ4_star_02_18
447
+ transitions:
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+ IGHJ4_star_02_19: 1.0
449
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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