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/hmm/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: 0.08760869565217394
5
+ per_gene_mute_freq: 0.10848778633067233
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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: 0.09398496240601503
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+ insert_left_C: 0.16917293233082706
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+ insert_left_G: 0.11654135338345864
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+ insert_left_T: 0.12030075187969924
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.8915122136693276
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+ C: 0.03616259544355744
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+ G: 0.03616259544355744
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+ T: 0.03616259544355744
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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: 0.09398496240601503
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+ insert_left_C: 0.16917293233082706
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+ insert_left_G: 0.11654135338345864
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+ insert_left_T: 0.12030075187969924
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.03616259544355744
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+ C: 0.8915122136693276
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+ G: 0.03616259544355744
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+ T: 0.03616259544355744
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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:
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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: 0.09398496240601503
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+ insert_left_C: 0.16917293233082706
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+ insert_left_G: 0.11654135338345864
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+ insert_left_T: 0.12030075187969924
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ C: 0.03616259544355744
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
147
+ 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: 0.09398496240601503
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+ insert_left_C: 0.16917293233082706
181
+ insert_left_G: 0.11654135338345864
182
+ insert_left_T: 0.12030075187969924
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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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: 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_10: 0.017857142857142856
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+ IGHD2-21_star_02_17: 0.017857142857142856
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+ IGHD2-21_star_02_26: 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: 0.16917293233082706
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+ insert_left_G: 0.11654135338345864
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+ insert_left_T: 0.12030075187969924
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: A
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+ name: IGHD2-21_star_02_0
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+ transitions:
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+ IGHD2-21_star_02_1: 0.9642857142857143
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ transitions:
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ end: 0.03571428571428571
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+ - !!python/object:python.hmmwriter.State
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+ - !!python/object:python.hmmwriter.State
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379
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380
+ track: nukes
381
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382
+ ambiguous_char: N
383
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384
+ germline: T
385
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386
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387
+ IGHD2-21_star_02_10: 0.9642857142857143
388
+ end: 0.03571428571428571
389
+ - !!python/object:python.hmmwriter.State
390
+ emissions:
391
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392
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393
+ C: 0.03587185532259167
394
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395
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396
+ track: nukes
397
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398
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399
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400
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401
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402
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403
+ IGHD2-21_star_02_11: 0.9642857142857143
404
+ end: 0.03571428571428571
405
+ - !!python/object:python.hmmwriter.State
406
+ emissions:
407
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408
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409
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410
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411
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412
+ track: nukes
413
+ extras:
414
+ ambiguous_char: N
415
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416
+ germline: G
417
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418
+ transitions:
419
+ IGHD2-21_star_02_12: 0.9642857142857143
420
+ end: 0.03571428571428571
421
+ - !!python/object:python.hmmwriter.State
422
+ emissions:
423
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424
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425
+ C: 0.03587185532259167
426
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427
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428
+ track: nukes
429
+ extras:
430
+ ambiguous_char: N
431
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432
+ germline: T
433
+ name: IGHD2-21_star_02_12
434
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435
+ IGHD2-21_star_02_13: 0.9642857142857143
436
+ end: 0.03571428571428571
437
+ - !!python/object:python.hmmwriter.State
438
+ emissions:
439
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440
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441
+ C: 0.03587185532259167
442
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443
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444
+ track: nukes
445
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446
+ ambiguous_char: N
447
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448
+ germline: G
449
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450
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451
+ IGHD2-21_star_02_14: 0.9642857142857143
452
+ end: 0.03571428571428571
453
+ - !!python/object:python.hmmwriter.State
454
+ emissions:
455
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456
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457
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458
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459
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460
+ track: nukes
461
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462
+ ambiguous_char: N
463
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464
+ germline: G
465
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466
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467
+ IGHD2-21_star_02_15: 0.9642857142857143
468
+ end: 0.03571428571428571
469
+ - !!python/object:python.hmmwriter.State
470
+ emissions:
471
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472
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473
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474
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475
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476
+ track: nukes
477
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478
+ ambiguous_char: N
479
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480
+ germline: T
481
+ name: IGHD2-21_star_02_15
482
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483
+ IGHD2-21_star_02_16: 0.9642857142857143
484
+ end: 0.03571428571428571
485
+ - !!python/object:python.hmmwriter.State
486
+ emissions:
487
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488
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489
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490
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491
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492
+ track: nukes
493
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494
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495
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496
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497
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498
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499
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500
+ end: 0.03571428571428571
501
+ - !!python/object:python.hmmwriter.State
502
+ emissions:
503
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504
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505
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506
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507
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508
+ track: nukes
509
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510
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511
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512
+ germline: A
513
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514
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515
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516
+ end: 0.03571428571428571
517
+ - !!python/object:python.hmmwriter.State
518
+ emissions:
519
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520
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521
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522
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523
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524
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525
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526
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527
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528
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529
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530
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531
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532
+ end: 0.03571428571428571
533
+ - !!python/object:python.hmmwriter.State
534
+ emissions:
535
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536
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537
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538
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539
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540
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541
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542
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543
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544
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545
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546
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547
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548
+ end: 0.03571428571428571
549
+ - !!python/object:python.hmmwriter.State
550
+ emissions:
551
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552
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553
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554
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555
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556
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557
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558
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559
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560
+ germline: G
561
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562
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563
+ IGHD2-21_star_02_21: 0.9642857142857143
564
+ end: 0.03571428571428571
565
+ - !!python/object:python.hmmwriter.State
566
+ emissions:
567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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578
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579
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580
+ end: 0.03571428571428571
581
+ - !!python/object:python.hmmwriter.State
582
+ emissions:
583
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584
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585
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586
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587
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588
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589
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590
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591
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592
+ germline: T
593
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594
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595
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596
+ end: 0.03571428571428571
597
+ - !!python/object:python.hmmwriter.State
598
+ emissions:
599
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600
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601
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602
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603
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604
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605
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606
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607
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608
+ germline: A
609
+ name: IGHD2-21_star_02_23
610
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611
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612
+ end: 0.03571428571428571
613
+ - !!python/object:python.hmmwriter.State
614
+ emissions:
615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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628
+ end: 0.03571428571428571
629
+ - !!python/object:python.hmmwriter.State
630
+ emissions:
631
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632
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633
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634
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635
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636
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637
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638
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639
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640
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641
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642
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643
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644
+ end: 0.03571428571428571
645
+ - !!python/object:python.hmmwriter.State
646
+ emissions:
647
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648
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649
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650
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651
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652
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653
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654
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655
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656
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657
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658
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659
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660
+ end: 0.03571428571428571
661
+ - !!python/object:python.hmmwriter.State
662
+ emissions:
663
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664
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665
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666
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667
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668
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669
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670
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671
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672
+ germline: C
673
+ name: IGHD2-21_star_02_27
674
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675
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676
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677
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678
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679
+ - C
680
+ - G
681
+ - T