partis-bcr 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.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 (139) hide show
  1. bin/partis-test.py +4 -1
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/partis-test.py +4 -1
  4. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/METADATA +2 -1
  5. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/RECORD +98 -139
  6. python/utils.py +1 -1
  7. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  8. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  9. test/new-results/test/parameters/simu/hmm/all-probs.csv +3 -13
  10. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  11. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  12. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  13. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +1 -6
  14. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +2 -9
  15. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +1 -5
  16. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +2 -10
  17. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  18. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +2 -3
  19. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +0 -6
  20. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +0 -8
  21. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +0 -2
  22. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +0 -10
  23. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +268 -267
  24. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  25. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  26. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  27. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  28. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  29. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  30. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +2 -9
  31. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +1 -2
  32. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +2 -7
  33. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +1 -2
  34. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  35. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +13 -16
  36. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +40 -44
  37. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +0 -2
  38. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +291 -293
  39. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  40. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  41. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  42. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +1 -6
  43. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +1 -7
  44. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +1 -6
  45. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  46. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  47. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  48. test/new-results/test/parameters/simu/sw/all-probs.csv +1 -9
  49. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  50. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  51. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  52. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +1 -7
  53. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +1 -7
  54. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +1 -5
  55. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +1 -8
  56. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  57. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  58. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +0 -6
  59. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +0 -8
  60. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +0 -2
  61. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +0 -10
  62. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +268 -267
  63. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  64. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  65. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  66. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  67. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  68. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  69. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +1 -7
  70. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +1 -2
  71. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +1 -7
  72. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +1 -2
  73. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  74. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +13 -16
  75. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +40 -48
  76. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +291 -293
  77. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  78. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  79. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  80. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +1 -6
  81. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +1 -7
  82. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +1 -6
  83. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  84. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  85. test/new-results/test.log +24 -258
  86. test/test.py +4 -1
  87. bin/partis-pip +0 -116
  88. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +0 -449
  89. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +0 -870
  90. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +0 -744
  91. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +0 -534
  92. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +0 -986
  93. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +0 -4484
  94. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +0 -4484
  95. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +0 -4438
  96. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +0 -4529
  97. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +0 -4484
  98. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +0 -9
  99. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +0 -30
  100. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +0 -32
  101. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +0 -22
  102. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +0 -50
  103. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +0 -297
  104. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +0 -297
  105. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +0 -291
  106. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +0 -300
  107. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +0 -296
  108. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +0 -449
  109. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +0 -870
  110. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +0 -744
  111. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +0 -534
  112. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +0 -986
  113. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +0 -4484
  114. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +0 -4484
  115. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +0 -4438
  116. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +0 -4529
  117. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +0 -4484
  118. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +0 -9
  119. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +0 -30
  120. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +0 -32
  121. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +0 -20
  122. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +0 -50
  123. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +0 -297
  124. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +0 -297
  125. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +0 -291
  126. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +0 -300
  127. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +0 -296
  128. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-alleles.py +0 -0
  129. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/cf-germlines.py +0 -0
  130. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/compare-plotdirs.py +0 -0
  131. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/extract-pairing-info.py +0 -0
  132. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/gctree-run.py +0 -0
  133. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/get-naive-probabilities.py +0 -0
  134. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/parse-output.py +0 -0
  135. {partis_bcr-1.0.5.data → partis_bcr-1.0.7.data}/scripts/split-loci.py +0 -0
  136. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/WHEEL +0 -0
  137. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/entry_points.txt +0 -0
  138. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/licenses/COPYING +0 -0
  139. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv DELETED
@@ -1,9 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
- 3,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
3
- 4,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
4
- 5,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
5
- 6,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
6
- 7,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
7
- 8,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
8
- 9,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
9
- 10,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv DELETED
@@ -1,30 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
2
- 8,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
3
- 9,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
4
- 10,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
5
- 11,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
6
- 12,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
7
- 13,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
8
- 14,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
9
- 15,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
10
- 16,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
11
- 17,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
12
- 18,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
13
- 19,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
14
- 20,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
15
- 21,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
16
- 22,0.0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511
17
- 23,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0,0.0,0,0.0,0.481701970511
18
- 24,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
19
- 25,0.0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,0.0,0,0.0,0.481701970511,1.0,2,0.6933612743506348,1.0
20
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test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv DELETED
@@ -1,32 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
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test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv DELETED
@@ -1,20 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
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test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv DELETED
@@ -1,50 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
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test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv DELETED
@@ -1,297 +0,0 @@
1
- position,mute_freq,lo_err,hi_err,A,A_obs,A_lo_err,A_hi_err,C,C_obs,C_lo_err,C_hi_err,G,G_obs,G_lo_err,G_hi_err,T,T_obs,T_lo_err,T_hi_err
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80
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81
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87
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88
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89
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90
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91
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92
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94
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96
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98
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99
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100
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101
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102
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103
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104
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105
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107
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108
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109
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
- 125,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
128
- 126,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
129
- 127,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
130
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131
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