partis-bcr 1.0.5__py3-none-any.whl → 1.0.6__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 (137) hide show
  1. bin/partis-test.py +4 -1
  2. packages/ham/bcrham +0 -0
  3. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/partis-test.py +4 -1
  4. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/METADATA +1 -1
  5. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/RECORD +97 -137
  6. test/new-results/test/parameters/simu/hmm/all-mean-mute-freqs.csv +3 -3
  7. test/new-results/test/parameters/simu/hmm/all-mean-n-muted.csv +11 -11
  8. test/new-results/test/parameters/simu/hmm/all-probs.csv +3 -13
  9. test/new-results/test/parameters/simu/hmm/cluster_size.csv +1 -1
  10. test/new-results/test/parameters/simu/hmm/d-mean-mute-freqs.csv +6 -6
  11. test/new-results/test/parameters/simu/hmm/d-mean-n-muted.csv +3 -3
  12. test/new-results/test/parameters/simu/hmm/d_gene-d_3p_del-probs.csv +1 -6
  13. test/new-results/test/parameters/simu/hmm/d_gene-d_5p_del-probs.csv +2 -9
  14. test/new-results/test/parameters/simu/hmm/d_gene-probs.csv +1 -5
  15. test/new-results/test/parameters/simu/hmm/d_gene-vd_insertion-probs.csv +2 -10
  16. test/new-results/test/parameters/simu/hmm/dj_insertion_content.csv +4 -4
  17. test/new-results/test/parameters/simu/hmm/fv_insertion-probs.csv +2 -3
  18. test/new-results/test/parameters/simu/hmm/germline-sets/igh/extras.csv +0 -6
  19. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighd.fasta +0 -8
  20. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighj.fasta +0 -2
  21. test/new-results/test/parameters/simu/hmm/germline-sets/igh/ighv.fasta +0 -10
  22. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-13_star_01.yaml +268 -267
  23. test/new-results/test/parameters/simu/hmm/hmms/IGHJ4_star_02.yaml +306 -306
  24. test/new-results/test/parameters/simu/hmm/hmms/IGHJ6_star_02.yaml +284 -284
  25. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-66_star_02.yaml +1191 -1191
  26. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-7_star_05.yaml +2 -2
  27. test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv +5 -5
  28. test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv +4 -4
  29. test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv +2 -9
  30. test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv +1 -2
  31. test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv +2 -7
  32. test/new-results/test/parameters/simu/hmm/j_gene-probs.csv +1 -2
  33. test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv +1 -1
  34. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv +13 -16
  35. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv +40 -44
  36. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv +0 -2
  37. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-66_star_02.csv +291 -293
  38. test/new-results/test/parameters/simu/hmm/seq_content.csv +4 -4
  39. test/new-results/test/parameters/simu/hmm/v-mean-mute-freqs.csv +3 -3
  40. test/new-results/test/parameters/simu/hmm/v-mean-n-muted.csv +7 -7
  41. test/new-results/test/parameters/simu/hmm/v_gene-probs.csv +1 -6
  42. test/new-results/test/parameters/simu/hmm/v_gene-v_3p_del-probs.csv +1 -7
  43. test/new-results/test/parameters/simu/hmm/v_gene-v_5p_del-probs.csv +1 -6
  44. test/new-results/test/parameters/simu/hmm/vd_insertion_content.csv +4 -4
  45. test/new-results/test/parameters/simu/sw/all-mean-mute-freqs.csv +3 -3
  46. test/new-results/test/parameters/simu/sw/all-mean-n-muted.csv +8 -8
  47. test/new-results/test/parameters/simu/sw/all-probs.csv +1 -9
  48. test/new-results/test/parameters/simu/sw/cluster_size.csv +1 -1
  49. test/new-results/test/parameters/simu/sw/d-mean-mute-freqs.csv +5 -5
  50. test/new-results/test/parameters/simu/sw/d-mean-n-muted.csv +3 -3
  51. test/new-results/test/parameters/simu/sw/d_gene-d_3p_del-probs.csv +1 -7
  52. test/new-results/test/parameters/simu/sw/d_gene-d_5p_del-probs.csv +1 -7
  53. test/new-results/test/parameters/simu/sw/d_gene-probs.csv +1 -5
  54. test/new-results/test/parameters/simu/sw/d_gene-vd_insertion-probs.csv +1 -8
  55. test/new-results/test/parameters/simu/sw/dj_insertion_content.csv +4 -4
  56. test/new-results/test/parameters/simu/sw/fv_insertion-probs.csv +1 -1
  57. test/new-results/test/parameters/simu/sw/germline-sets/igh/extras.csv +0 -6
  58. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighd.fasta +0 -8
  59. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighj.fasta +0 -2
  60. test/new-results/test/parameters/simu/sw/germline-sets/igh/ighv.fasta +0 -10
  61. test/new-results/test/parameters/simu/sw/hmms/IGHD6-13_star_01.yaml +268 -267
  62. test/new-results/test/parameters/simu/sw/hmms/IGHJ4_star_02.yaml +306 -306
  63. test/new-results/test/parameters/simu/sw/hmms/IGHJ6_star_02.yaml +22 -22
  64. test/new-results/test/parameters/simu/sw/hmms/IGHV3-66_star_02.yaml +1191 -1191
  65. test/new-results/test/parameters/simu/sw/hmms/IGHV3-7_star_05.yaml +2 -2
  66. test/new-results/test/parameters/simu/sw/j-mean-mute-freqs.csv +4 -4
  67. test/new-results/test/parameters/simu/sw/j-mean-n-muted.csv +3 -3
  68. test/new-results/test/parameters/simu/sw/j_gene-dj_insertion-probs.csv +1 -7
  69. test/new-results/test/parameters/simu/sw/j_gene-j_3p_del-probs.csv +1 -2
  70. test/new-results/test/parameters/simu/sw/j_gene-j_5p_del-probs.csv +1 -7
  71. test/new-results/test/parameters/simu/sw/j_gene-probs.csv +1 -2
  72. test/new-results/test/parameters/simu/sw/jf_insertion-probs.csv +1 -1
  73. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-13_star_01.csv +13 -16
  74. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ4_star_02.csv +40 -48
  75. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-66_star_02.csv +291 -293
  76. test/new-results/test/parameters/simu/sw/seq_content.csv +4 -4
  77. test/new-results/test/parameters/simu/sw/v-mean-mute-freqs.csv +3 -3
  78. test/new-results/test/parameters/simu/sw/v-mean-n-muted.csv +7 -7
  79. test/new-results/test/parameters/simu/sw/v_gene-probs.csv +1 -6
  80. test/new-results/test/parameters/simu/sw/v_gene-v_3p_del-probs.csv +1 -7
  81. test/new-results/test/parameters/simu/sw/v_gene-v_5p_del-probs.csv +1 -6
  82. test/new-results/test/parameters/simu/sw/vd_insertion_content.csv +4 -4
  83. test/new-results/test/parameters/simu/sw-cache.yaml +1 -1
  84. test/new-results/test.log +24 -258
  85. test/test.py +4 -1
  86. test/new-results/test/parameters/simu/hmm/hmms/IGHD1-20_star_01.yaml +0 -449
  87. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-16_star_02.yaml +0 -870
  88. test/new-results/test/parameters/simu/hmm/hmms/IGHD3-22_star_01.yaml +0 -744
  89. test/new-results/test/parameters/simu/hmm/hmms/IGHD6-19_star_01.yaml +0 -534
  90. test/new-results/test/parameters/simu/hmm/hmms/IGHJ1_star_01.yaml +0 -986
  91. test/new-results/test/parameters/simu/hmm/hmms/IGHV1-18_star_01.yaml +0 -4484
  92. test/new-results/test/parameters/simu/hmm/hmms/IGHV3-23_star_01.yaml +0 -4484
  93. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-4_star_09.yaml +0 -4438
  94. test/new-results/test/parameters/simu/hmm/hmms/IGHV4-61_star_01.yaml +0 -4529
  95. test/new-results/test/parameters/simu/hmm/hmms/IGHV5-51_star_01.yaml +0 -4484
  96. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD1-20_star_01.csv +0 -9
  97. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-16_star_02.csv +0 -30
  98. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD3-22_star_01.csv +0 -32
  99. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-19_star_01.csv +0 -22
  100. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ1_star_01.csv +0 -50
  101. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV1-18_star_01.csv +0 -297
  102. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV3-23_star_01.csv +0 -297
  103. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-4_star_09.csv +0 -291
  104. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV4-61_star_01.csv +0 -300
  105. test/new-results/test/parameters/simu/hmm/mute-freqs/IGHV5-51_star_01.csv +0 -296
  106. test/new-results/test/parameters/simu/sw/hmms/IGHD1-20_star_01.yaml +0 -449
  107. test/new-results/test/parameters/simu/sw/hmms/IGHD3-16_star_02.yaml +0 -870
  108. test/new-results/test/parameters/simu/sw/hmms/IGHD3-22_star_01.yaml +0 -744
  109. test/new-results/test/parameters/simu/sw/hmms/IGHD6-19_star_01.yaml +0 -534
  110. test/new-results/test/parameters/simu/sw/hmms/IGHJ1_star_01.yaml +0 -986
  111. test/new-results/test/parameters/simu/sw/hmms/IGHV1-18_star_01.yaml +0 -4484
  112. test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml +0 -4484
  113. test/new-results/test/parameters/simu/sw/hmms/IGHV4-4_star_09.yaml +0 -4438
  114. test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml +0 -4529
  115. test/new-results/test/parameters/simu/sw/hmms/IGHV5-51_star_01.yaml +0 -4484
  116. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD1-20_star_01.csv +0 -9
  117. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-16_star_02.csv +0 -30
  118. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD3-22_star_01.csv +0 -32
  119. test/new-results/test/parameters/simu/sw/mute-freqs/IGHD6-19_star_01.csv +0 -20
  120. test/new-results/test/parameters/simu/sw/mute-freqs/IGHJ1_star_01.csv +0 -50
  121. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV1-18_star_01.csv +0 -297
  122. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV3-23_star_01.csv +0 -297
  123. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-4_star_09.csv +0 -291
  124. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv +0 -300
  125. test/new-results/test/parameters/simu/sw/mute-freqs/IGHV5-51_star_01.csv +0 -296
  126. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/cf-alleles.py +0 -0
  127. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/cf-germlines.py +0 -0
  128. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/compare-plotdirs.py +0 -0
  129. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/extract-pairing-info.py +0 -0
  130. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/gctree-run.py +0 -0
  131. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/get-naive-probabilities.py +0 -0
  132. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/parse-output.py +0 -0
  133. {partis_bcr-1.0.5.data → partis_bcr-1.0.6.data}/scripts/split-loci.py +0 -0
  134. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/WHEEL +0 -0
  135. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/entry_points.txt +0 -0
  136. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/licenses/COPYING +0 -0
  137. {partis_bcr-1.0.5.dist-info → partis_bcr-1.0.6.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/mute-freqs/IGHV4-61_star_01.csv DELETED
@@ -1,300 +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
- 0,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
3
- 1,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
4
- 2,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
5
- 3,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
6
- 4,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
7
- 5,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
8
- 6,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
9
- 7,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
10
- 8,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
11
- 9,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
12
- 10,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
13
- 11,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
14
- 12,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
15
- 13,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
16
- 14,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
17
- 15,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
18
- 16,0.0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
19
- 17,0.125,0.082581398133,0.317494100505,0.0,0,0.0,0.234912702372,0.125,1,0.082581398133,0.317494100505,0.875,7,0.682505899495,0.917418601867,0.0,0,0.0,0.234912702372
20
- 18,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0
21
- 19,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
22
- 20,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
23
- 21,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
24
- 22,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372
25
- 23,0.125,0.082581398133,0.317494100505,0.125,1,0.082581398133,0.317494100505,0.875,7,0.682505899495,0.917418601867,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
26
- 24,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
27
- 25,0.0,0.0,0.234912702372,0.0,0,0.0,0.234912702372,1.0,8,0.8850881520714603,1.0,0.0,0,0.0,0.234912702372,0.0,0,0.0,0.234912702372
28
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108
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