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/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg CHANGED
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@@ -127,7 +127,7 @@ L -3.5 0
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@@ -137,7 +137,7 @@ L -3.5 0
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@@ -161,25 +161,25 @@ L -3.5 0
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@@ -234,7 +234,7 @@ L 145.13664 108.8308
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235
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236
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238
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@@ -244,7 +244,7 @@ L 145.13664 108.8308
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248
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249
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250
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test/paired/new-results/run-times.csv CHANGED
@@ -1,7 +1,7 @@
1
1
  name,seconds
2
- cache-parameters-simu,19.6
3
- partition-new-simu,31.1
4
- subset-partition-new-simu,113.4
5
- seed-partition-new-simu,17.2
6
- get-selection-metrics-new-simu,10.5
7
- cache-parameters-data,33.8
2
+ cache-parameters-simu,34.9
3
+ partition-new-simu,36.9
4
+ subset-partition-new-simu,135.7
5
+ seed-partition-new-simu,19.8
6
+ get-selection-metrics-new-simu,14.1
7
+ cache-parameters-data,40.6
test/paired/new-results/subset-partition-new-simu/isub-0/partition.log CHANGED
@@ -43,30 +43,30 @@ smith-waterman (new-allele fitting)
43
43
  running 10 procs for 24 seqs
44
44
  info for 24 / 24 = 1.000 (removed: 0 failed)
45
45
  kept 11 (0.458) unproductive
46
- water time: 0.2 (ig-sw 0.0 processing 0.1)
46
+ water time: 0.2 (ig-sw 0.0 processing 0.2)
47
47
  smith-waterman (writing parameters)
48
48
  vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
49
49
  running 10 procs for 24 seqs
50
50
  info for 24 / 24 = 1.000 (removed: 0 failed)
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
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (0.8 sec)
54
- water time: 1.0 (ig-sw 0.9 processing 0.1)
53
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (1.0 sec)
54
+ water time: 1.2 (ig-sw 1.1 processing 0.2)
55
55
  writing hmms removed 21 genes from glfo (leaving v 6 d 13 j 4)
56
56
 
57
57
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
58
- (0.6 sec)
58
+ (0.9 sec)
59
59
  hmm
60
60
  reading output
61
61
  read 24 hmm output lines with 24 sequences in 24 events (0 failures)
62
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.7 sec)
63
- infra time: 0.8
64
- hmm step time: 1.3
62
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.1 sec)
63
+ infra time: 1.2
64
+ hmm step time: 1.8
65
65
  writing hmms removed 4 genes from glfo (leaving v 6 d 9 j 4)
66
66
 
67
67
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
68
- (0.6 sec)
69
- total time: 4.1
68
+ (0.7 sec)
69
+ total time: 5.2
70
70
  cache-parameters igk:
71
71
  run partis cache-parameters --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 --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
72
72
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -74,7 +74,7 @@ caching parameters
74
74
  vsearch: 18 / 18 v annotations (0 failed) with 6 v genes in 0.1 sec
75
75
  keeping 5 / 64 v genes
76
76
  smith-waterman (new-allele fitting)
77
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
77
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
78
78
  running 10 procs for 18 seqs
79
79
  running 11 procs for 2 seqs
80
80
  info for 18 / 18 = 1.000 (removed: 0 failed)
@@ -87,23 +87,23 @@ smith-waterman (writing parameters)
87
87
  info for 18 / 18 = 1.000 (removed: 0 failed)
88
88
  kept 5 (0.278) unproductive
89
89
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
90
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.6 sec)
90
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.7 sec)
91
91
  water time: 1.0 (ig-sw 0.7 processing 0.1)
92
92
  writing hmms removed 2 genes from glfo (leaving v 5 d 1 j 5)
93
93
 
94
94
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
95
- (0.4 sec)
95
+ (0.5 sec)
96
96
  hmm
97
97
  reading output
98
98
  read 18 hmm output lines with 18 sequences in 18 events (0 failures)
99
99
  writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.6 sec)
100
100
  infra time: 0.7
101
- hmm step time: 1.0
101
+ hmm step time: 1.1
102
102
  writing hmms removed 0 genes from glfo (leaving v 5 d 1 j 5)
103
103
 
104
104
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
105
105
  (0.4 sec)
106
- total time: 3.5
106
+ total time: 3.8
107
107
  cache-parameters igl:
108
108
  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
109
109
  --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -122,8 +122,8 @@ smith-waterman (writing parameters)
122
122
  info for 10 / 10 = 1.000 (removed: 0 failed)
123
123
  kept 7 (0.700) unproductive
124
124
  writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
125
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.4 sec)
126
- water time: 0.6 (ig-sw 0.5 processing 0.1)
125
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.5 sec)
126
+ water time: 0.7 (ig-sw 0.6 processing 0.2)
127
127
  writing hmms removed 7 genes from glfo (leaving v 3 d 1 j 2)
128
128
 
129
129
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -131,14 +131,14 @@ smith-waterman (writing parameters)
131
131
  hmm
132
132
  reading output
133
133
  read 10 hmm output lines with 10 sequences in 10 events (0 failures)
134
- writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.3 sec)
135
- infra time: 0.4
136
- hmm step time: 0.7
134
+ writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.5 sec)
135
+ infra time: 0.5
136
+ hmm step time: 0.8
137
137
  writing hmms removed 0 genes from glfo (leaving v 3 d 1 j 2)
138
138
 
139
139
  note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
140
140
  (0.2 sec)
141
- total time: 2.2
141
+ total time: 2.6
142
142
  partition igh:
143
143
  run partis partition --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/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/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
144
144
  --input-metafnames: added meta info for 24 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -150,20 +150,20 @@ smith-waterman
150
150
  kept 11 (0.458) unproductive
151
151
  water time: 0.0
152
152
  hmm
153
- caching all 24 naive sequences (0.5s)
153
+ caching all 24 naive sequences (0.6s)
154
154
  collapsed 24 queries into 22 clusters with identical naive seqs (0.0 sec)
155
155
  22 clusters with 10 procs (0.4s)
156
- 22 clusters with 7 procs (0.3s)
157
- 20 clusters with 5 procs (0.3s)
158
- 18 clusters with 3 procs (0.4s)
156
+ 22 clusters with 7 procs (0.4s)
157
+ 20 clusters with 5 procs (0.4s)
158
+ 18 clusters with 3 procs (0.5s)
159
159
  14 clusters with 2 procs (0.4s)
160
- 12 clusters with 1 proc (0.3s)
160
+ 12 clusters with 1 proc (0.4s)
161
161
  note not merging entire cpath history
162
- partition loop time: 2.2
162
+ partition loop time: 2.4
163
163
  getting annotations for final partition
164
- subcluster annotating 12 clusters with steps: (0.4s) (0.2s)
165
- subcluster annotation time 0.6
166
- total time: 3.5
164
+ subcluster annotating 12 clusters with steps: (0.5s) (0.3s)
165
+ subcluster annotation time 0.7
166
+ total time: 3.9
167
167
  partition igk:
168
168
  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
169
169
  --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -182,7 +182,7 @@ hmm
182
182
  7 clusters with 5 procs (0.3s)
183
183
  7 clusters with 3 procs (0.2s)
184
184
  7 clusters with 2 procs (0.2s)
185
- 7 clusters with 1 proc (0.3s)
185
+ 7 clusters with 1 proc (0.4s)
186
186
  partition loop time: 1.3
187
187
  getting annotations for final partition
188
188
  subcluster annotating 6 clusters with steps: (0.3s) (0.2s)
@@ -193,7 +193,7 @@ getting annotations for final partition
193
193
  --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
194
194
  partitioning (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
195
195
  smith-waterman
196
- vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
196
+ vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
197
197
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
198
198
  info for 10 / 10 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
199
199
  kept 7 (0.700) unproductive
@@ -204,12 +204,12 @@ hmm
204
204
  reducing n procs to number of clusters: 10 --> 3
205
205
  3 clusters with 3 procs (0.2s)
206
206
  3 clusters with 2 procs (0.2s)
207
- 3 clusters with 1 proc (0.3s)
207
+ 3 clusters with 1 proc (0.2s)
208
208
  partition loop time: 0.6
209
209
  getting annotations for final partition
210
- subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
211
- subcluster annotation time 0.3
212
- total time: 1.4
210
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
211
+ subcluster annotation time 0.4
212
+ total time: 1.5
213
213
  combining chains
214
214
  cleaning pair info for 52 seqs
215
215
  synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0 k 0 l 0
@@ -229,6 +229,7 @@ cleaning pair info for 52 seqs
229
229
  k 0 0 3
230
230
  merge time 0.0
231
231
  need to get annotations for 1/8 joint igh clusters
232
+ tag: v1.0.12
232
233
  annotate igh+igk: igh
233
234
  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
234
235
  --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
@@ -241,17 +242,18 @@ smith-waterman
241
242
  kept 6 (0.375) unproductive
242
243
  water time: 0.0
243
244
  hmm
244
- subcluster annotating 8 clusters with steps: (0.3s) (0.1s)
245
- subcluster annotation time 0.5
246
- total time: 0.7
245
+ subcluster annotating 8 clusters with steps: (0.6s) (0.3s)
246
+ subcluster annotation time 0.9
247
+ total time: 1.1
247
248
  need to get annotations for 5/8 joint igk clusters
249
+ tag: v1.0.12
248
250
  annotate igh+igk: igk
249
251
  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
250
252
  --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
251
253
  --input-partition-fname: read best partition with 18 sequences in 8 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
252
254
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
253
255
  smith-waterman
254
- vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
256
+ vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
255
257
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
256
258
  info for 18 / 18 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
257
259
  kept 5 (0.278) unproductive
@@ -259,7 +261,7 @@ smith-waterman
259
261
  hmm
260
262
  subcluster annotating 8 clusters with steps: (0.3s) (0.2s)
261
263
  subcluster annotation time 0.5
262
- total time: 0.6
264
+ total time: 0.7
263
265
  igh+igl: synchronizing heavy and light chain cluster paths
264
266
  removing badly + unpaired seqs: kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0 l 0
265
267
  note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -275,6 +277,7 @@ hmm
275
277
  h 0 0 0
276
278
  l 0 0 0
277
279
  merge time 0.0
280
+ tag: v1.0.12
278
281
  annotate igh+igl: igh
279
282
  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
280
283
  --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
@@ -288,10 +291,11 @@ smith-waterman
288
291
  kept 4 (0.571) unproductive
289
292
  water time: 0.0
290
293
  hmm
291
- subcluster annotating 3 clusters with steps: (0.2s) (0.3s)
292
- subcluster annotation time 0.5
293
- total time: 0.6
294
+ subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
295
+ subcluster annotation time 0.4
296
+ total time: 0.5
294
297
  need to get annotations for 2/3 joint igl clusters
298
+ tag: v1.0.12
295
299
  annotate igh+igl: igl
296
300
  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
297
301
  --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
@@ -299,13 +303,13 @@ hmm
299
303
  --input-partition-fname: read best partition with 7 sequences in 3 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igl-only-partition.yaml
300
304
  annotating (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
301
305
  smith-waterman
302
- vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.1 sec
306
+ vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.2 sec
303
307
  reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
304
308
  info for 7 / 7 = 1.000 (removed: 0 failed, 0 duplicates [removed when cache file was written])
305
309
  kept 6 (0.857) unproductive
306
310
  water time: 0.0
307
311
  hmm
308
- subcluster annotating 3 clusters with steps: (0.2s) (0.2s)
312
+ subcluster annotating 3 clusters with steps: (0.2s) (0.1s)
309
313
  subcluster annotation time 0.4
310
314
  total time: 0.5
311
315
  --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml
@@ -320,4 +324,4 @@ hmm
320
324
  h 12 --> 11 -1
321
325
  k 6 --> 8 +2
322
326
  l 3 --> 3
323
- total time: 38.7
327
+ total time: 47.3