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/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg CHANGED
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test/paired/new-results/run-times.csv CHANGED
@@ -1,7 +1,8 @@
1
1
  name,seconds
2
- cache-parameters-simu,13.4
2
+ cache-parameters-simu,13.5
3
3
  partition-new-simu,21.2
4
- subset-partition-new-simu,69.4
5
- seed-partition-new-simu,10.5
4
+ subset-partition-new-simu,69.9
5
+ seed-partition-new-simu,10.6
6
6
  get-selection-metrics-new-simu,6.9
7
- cache-parameters-data,23.1
7
+ cache-parameters-data,23.4
8
+ simulate,24.2
test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -51,7 +51,7 @@ smith-waterman (writing parameters)
51
51
  kept 11 (0.458) unproductive
52
52
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
53
53
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (0.6 sec)
54
- water time: 0.6 (ig-sw 0.6 processing 0.0)
54
+ water time: 0.7 (ig-sw 0.6 processing 0.0)
55
55
  writing hmms removed 21 genes from glfo (leaving v 6 d 13 j 4)
56
56
  (0.5 sec)
57
57
  hmm
@@ -95,7 +95,7 @@ hmm
95
95
  hmm step time: 0.7
96
96
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
97
97
  (0.2 sec)
98
- total time: 1.8
98
+ total time: 1.9
99
99
  cache-parameters igl:
100
100
  run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
101
101
  --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -123,7 +123,7 @@ hmm
123
123
  read 10 hmm output lines with 10 sequences in 10 events (0 failures)
124
124
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.3 sec)
125
125
  infra time: 0.3
126
- hmm step time: 0.4
126
+ hmm step time: 0.5
127
127
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
128
128
  (0.1 sec)
129
129
  total time: 1.2
@@ -150,7 +150,7 @@ hmm
150
150
  partition loop time: 1.1
151
151
  getting annotations for final partition
152
152
  subcluster annotating 12 clusters with steps: (0.4s) (0.1s)
153
- subcluster annotation time 0.4
153
+ subcluster annotation time 0.5
154
154
  total time: 2.0
155
155
  partition igk:
156
156
  run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
@@ -217,7 +217,6 @@ cleaning pair info for 52 seqs
217
217
  k 0 0 3
218
218
  merge time 0.0
219
219
  need to get annotations for 1/8 joint igh clusters
220
- tag: v1.0.11
221
220
  annotate igh+igk: igh
222
221
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh-only-partition.yaml
223
222
  --input-metafnames: added meta info for 16 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igh.yaml: loci paired-uids
@@ -234,7 +233,6 @@ hmm
234
233
  subcluster annotation time 0.3
235
234
  total time: 0.4
236
235
  need to get annotations for 5/8 joint igk clusters
237
- tag: v1.0.11
238
236
  annotate igh+igk: igk
239
237
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
240
238
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml: loci paired-uids
@@ -265,7 +263,6 @@ hmm
265
263
  h 0 0 0
266
264
  l 0 0 0
267
265
  merge time 0.0
268
- tag: v1.0.11
269
266
  annotate igh+igl: igh
270
267
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
271
268
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igh.yaml: loci paired-uids
@@ -283,7 +280,6 @@ hmm
283
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  subcluster annotation time 0.2
284
281
  total time: 0.2
285
282
  need to get annotations for 2/3 joint igl clusters
286
- tag: v1.0.11
287
283
  annotate igh+igl: igl
288
284
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
289
285
  --input-metafnames: added meta info for 7 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/meta-igl.yaml: loci paired-uids
@@ -312,4 +308,4 @@ hmm
312
308
  h 12 --> 11 -1
313
309
  k 6 --> 8 +2
314
310
  l 3 --> 3
315
- total time: 23.9
311
+ total time: 24.0
test/paired/new-results/subset-partition-new-simu/isub-1/partition.log CHANGED
@@ -138,9 +138,9 @@ smith-waterman
138
138
  hmm
139
139
  caching all 32 naive sequences (0.6s)
140
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  collapsed 32 queries into 30 clusters with identical naive seqs (0.0 sec)
141
- 30 clusters with 10 procs (0.1s)
141
+ 30 clusters with 10 procs (0.2s)
142
142
  29 clusters with 7 procs (0.2s)
143
- 28 clusters with 5 procs (0.2s)
143
+ 28 clusters with 5 procs (0.3s)
144
144
  28 clusters with 3 procs (0.3s)
145
145
  23 clusters with 2 procs (0.3s)
146
146
  20 clusters with 1 proc (0.5s)
@@ -161,7 +161,7 @@ smith-waterman
161
161
  kept 9 (0.500) unproductive
162
162
  water time: 0.0
163
163
  hmm
164
- caching all 18 naive sequences (0.2s)
164
+ caching all 18 naive sequences (0.3s)
165
165
  collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
166
166
  reducing n procs to number of clusters: 10 --> 7
167
167
  7 clusters with 7 procs (0.0s)
@@ -215,7 +215,6 @@ cleaning pair info for 61 seqs
215
215
  k 0 0 1
216
216
  merge time 0.0
217
217
  need to get annotations for 2/11 joint igh clusters
218
- tag: v1.0.11
219
218
  annotate igh+igk: igh
220
219
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh-only-partition.yaml
221
220
  --input-metafnames: added meta info for 19 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igh.yaml: loci paired-uids
@@ -232,7 +231,6 @@ hmm
232
231
  subcluster annotation time 0.4
233
232
  total time: 0.5
234
233
  need to get annotations for 6/11 joint igk clusters
235
- tag: v1.0.11
236
234
  annotate igh+igk: igk
237
235
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igk-only-partition.yaml
238
236
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/meta-igk.yaml: loci paired-uids
@@ -265,7 +263,6 @@ hmm
265
263
  l 0 0 1
266
264
  merge time 0.0
267
265
  need to get annotations for 2/5 joint igh clusters
268
- tag: v1.0.11
269
266
  annotate igh+igl: igh
270
267
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igh/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igh-only-partition.yaml
271
268
  --input-metafnames: added meta info for 12 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igh.yaml: loci paired-uids
@@ -282,7 +279,6 @@ hmm
282
279
  subcluster annotation time 0.3
283
280
  total time: 0.4
284
281
  need to get annotations for 5/5 joint igl clusters
285
- tag: v1.0.11
286
282
  annotate igh+igl: igl
287
283
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-1/parameters/igl/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/partition-igl-only-partition.yaml
288
284
  --input-metafnames: added meta info for 11 sequences from test/paired/new-results/subset-partition-new-simu/isub-1/igh+igl/meta-igl.yaml: loci paired-uids
@@ -310,4 +306,4 @@ hmm
310
306
  h 16 --> 16
311
307
  k 6 --> 11 +5
312
308
  l 3 --> 5 +2
313
- total time: 25.3
309
+ total time: 25.4
test/paired/new-results/subset-partition-new-simu/merged-partition.log CHANGED
@@ -33,7 +33,7 @@ hmm
33
33
  22 clusters with 3 procs (0.3s)
34
34
  21 clusters with 2 procs (0.1s)
35
35
  21 clusters with 1 proc (0.4s)
36
- partition loop time: 1.8
36
+ partition loop time: 1.7
37
37
  getting annotations for final partition
38
38
  subcluster annotating 18 clusters with steps: (0.6s) (0.2s) (0.1s)
39
39
  subcluster annotation time 1.0
@@ -165,7 +165,6 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
165
165
  joint 0.963 0.594
166
166
  merge time 0.0
167
167
  need to get annotations for 6/15 joint igh clusters
168
- tag: v1.0.11
169
168
  annotate igh+igk: igh
170
169
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
171
170
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -179,11 +178,10 @@ smith-waterman
179
178
  kept 13 (0.371) unproductive
180
179
  water time: 0.0
181
180
  hmm
182
- subcluster annotating 15 clusters with steps: (0.5s) (0.1s)
183
- subcluster annotation time 0.6
181
+ subcluster annotating 15 clusters with steps: (0.4s) (0.1s)
182
+ subcluster annotation time 0.5
184
183
  total time: 0.6
185
184
  need to get annotations for 13/15 joint igk clusters
186
- tag: v1.0.11
187
185
  annotate igh+igk: igk
188
186
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
189
187
  run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igk/meta-igk.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml --ignore-sw-pair-info
@@ -228,7 +226,6 @@ hmm
228
226
  joint 1.000 0.787
229
227
  merge time 0.0
230
228
  need to get annotations for 2/6 joint igh clusters
231
- tag: v1.0.11
232
229
  annotate igh+igl: igh
233
230
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
234
231
  run partis annotate --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igh.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml --ignore-sw-pair-info
@@ -246,7 +243,6 @@ hmm
246
243
  subcluster annotation time 0.5
247
244
  total time: 0.6
248
245
  need to get annotations for 6/6 joint igl clusters
249
- tag: v1.0.11
250
246
  annotate igh+igl: igl
251
247
  removed 1 arg strs that were specific to action 'partition': --continue-from-input-partition
252
248
  run partis annotate --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/igh+igl/meta-igl.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl-only-partition.yaml --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile --infname test/paired/new-results/subset-partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/subset-partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml --ignore-sw-pair-info
@@ -276,4 +272,4 @@ hmm
276
272
  h 18 --> 21 +3
277
273
  k 6 --> 15 +9
278
274
  l 3 --> 6 +3
279
- total time: 15.2
275
+ total time: 15.3