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/hmm/hmms/IGHD1-20_star_01.yaml DELETED
@@ -1,449 +0,0 @@
1
- !!python/object:python.hmmwriter.HMM
2
- extras:
3
- gene_prob: 0.05555555555555555
4
- overall_mute_freq: 0.012499999999999999
5
- per_gene_mute_freq: 0.10662828165908236
6
- name: IGHD1-20_star_01
7
- states:
8
- - !!python/object:python.hmmwriter.State
9
- emissions: null
10
- extras: {}
11
- name: init
12
- transitions:
13
- IGHD1-20_star_01_0: 0.0196078431372549
14
- IGHD1-20_star_01_1: 0.0196078431372549
15
- IGHD1-20_star_01_10: 0.0196078431372549
16
- IGHD1-20_star_01_11: 0.0196078431372549
17
- IGHD1-20_star_01_12: 0.0196078431372549
18
- IGHD1-20_star_01_13: 0.0196078431372549
19
- IGHD1-20_star_01_14: 0.0196078431372549
20
- IGHD1-20_star_01_15: 0.0196078431372549
21
- IGHD1-20_star_01_16: 0.0196078431372549
22
- IGHD1-20_star_01_2: 0.0196078431372549
23
- IGHD1-20_star_01_3: 0.0392156862745098
24
- IGHD1-20_star_01_4: 0.026143790849673207
25
- IGHD1-20_star_01_5: 0.013071895424836605
26
- IGHD1-20_star_01_6: 4.353815782843751e-18
27
- IGHD1-20_star_01_7: 0.0196078431372549
28
- IGHD1-20_star_01_8: 0.0196078431372549
29
- IGHD1-20_star_01_9: 0.0196078431372549
30
- insert_left_A: 0.0756501182033097
31
- insert_left_C: 0.3026004728132388
32
- insert_left_G: 0.1087470449172577
33
- insert_left_T: 0.17966903073286053
34
- - !!python/object:python.hmmwriter.State
35
- emissions:
36
- probs:
37
- A: 0.8933717183409177
38
- C: 0.03554276055302746
39
- G: 0.03554276055302746
40
- T: 0.03554276055302746
41
- track: nukes
42
- extras:
43
- ambiguous_char: N
44
- ambiguous_emission_prob: 0.25
45
- germline: A
46
- name: insert_left_A
47
- transitions:
48
- IGHD1-20_star_01_0: 0.014705882352941176
49
- IGHD1-20_star_01_1: 0.014705882352941176
50
- IGHD1-20_star_01_10: 0.014705882352941176
51
- IGHD1-20_star_01_11: 0.014705882352941176
52
- IGHD1-20_star_01_12: 0.014705882352941176
53
- IGHD1-20_star_01_13: 0.014705882352941176
54
- IGHD1-20_star_01_14: 0.014705882352941176
55
- IGHD1-20_star_01_15: 0.014705882352941176
56
- IGHD1-20_star_01_16: 0.014705882352941176
57
- IGHD1-20_star_01_2: 0.014705882352941176
58
- IGHD1-20_star_01_3: 0.029411764705882353
59
- IGHD1-20_star_01_4: 0.019607843137254905
60
- IGHD1-20_star_01_5: 0.009803921568627454
61
- IGHD1-20_star_01_6: 3.2653618371328133e-18
62
- IGHD1-20_star_01_7: 0.014705882352941176
63
- IGHD1-20_star_01_8: 0.014705882352941176
64
- IGHD1-20_star_01_9: 0.014705882352941176
65
- insert_left_A: 0.0851063829787234
66
- insert_left_C: 0.3404255319148936
67
- insert_left_G: 0.1223404255319149
68
- insert_left_T: 0.2021276595744681
69
- - !!python/object:python.hmmwriter.State
70
- emissions:
71
- probs:
72
- A: 0.03554276055302746
73
- C: 0.8933717183409177
74
- G: 0.03554276055302746
75
- T: 0.03554276055302746
76
- track: nukes
77
- extras:
78
- ambiguous_char: N
79
- ambiguous_emission_prob: 0.25
80
- germline: C
81
- name: insert_left_C
82
- transitions:
83
- IGHD1-20_star_01_0: 0.014705882352941176
84
- IGHD1-20_star_01_1: 0.014705882352941176
85
- IGHD1-20_star_01_10: 0.014705882352941176
86
- IGHD1-20_star_01_11: 0.014705882352941176
87
- IGHD1-20_star_01_12: 0.014705882352941176
88
- IGHD1-20_star_01_13: 0.014705882352941176
89
- IGHD1-20_star_01_14: 0.014705882352941176
90
- IGHD1-20_star_01_15: 0.014705882352941176
91
- IGHD1-20_star_01_16: 0.014705882352941176
92
- IGHD1-20_star_01_2: 0.014705882352941176
93
- IGHD1-20_star_01_3: 0.029411764705882353
94
- IGHD1-20_star_01_4: 0.019607843137254905
95
- IGHD1-20_star_01_5: 0.009803921568627454
96
- IGHD1-20_star_01_6: 3.2653618371328133e-18
97
- IGHD1-20_star_01_7: 0.014705882352941176
98
- IGHD1-20_star_01_8: 0.014705882352941176
99
- IGHD1-20_star_01_9: 0.014705882352941176
100
- insert_left_A: 0.0851063829787234
101
- insert_left_C: 0.3404255319148936
102
- insert_left_G: 0.1223404255319149
103
- insert_left_T: 0.2021276595744681
104
- - !!python/object:python.hmmwriter.State
105
- emissions:
106
- probs:
107
- A: 0.03554276055302746
108
- C: 0.03554276055302746
109
- G: 0.8933717183409177
110
- T: 0.03554276055302746
111
- track: nukes
112
- extras:
113
- ambiguous_char: N
114
- ambiguous_emission_prob: 0.25
115
- germline: G
116
- name: insert_left_G
117
- transitions:
118
- IGHD1-20_star_01_0: 0.014705882352941176
119
- IGHD1-20_star_01_1: 0.014705882352941176
120
- IGHD1-20_star_01_10: 0.014705882352941176
121
- IGHD1-20_star_01_11: 0.014705882352941176
122
- IGHD1-20_star_01_12: 0.014705882352941176
123
- IGHD1-20_star_01_13: 0.014705882352941176
124
- IGHD1-20_star_01_14: 0.014705882352941176
125
- IGHD1-20_star_01_15: 0.014705882352941176
126
- IGHD1-20_star_01_16: 0.014705882352941176
127
- IGHD1-20_star_01_2: 0.014705882352941176
128
- IGHD1-20_star_01_3: 0.029411764705882353
129
- IGHD1-20_star_01_4: 0.019607843137254905
130
- IGHD1-20_star_01_5: 0.009803921568627454
131
- IGHD1-20_star_01_6: 3.2653618371328133e-18
132
- IGHD1-20_star_01_7: 0.014705882352941176
133
- IGHD1-20_star_01_8: 0.014705882352941176
134
- IGHD1-20_star_01_9: 0.014705882352941176
135
- insert_left_A: 0.0851063829787234
136
- insert_left_C: 0.3404255319148936
137
- insert_left_G: 0.1223404255319149
138
- insert_left_T: 0.2021276595744681
139
- - !!python/object:python.hmmwriter.State
140
- emissions:
141
- probs:
142
- A: 0.03554276055302746
143
- C: 0.03554276055302746
144
- G: 0.03554276055302746
145
- T: 0.8933717183409177
146
- track: nukes
147
- extras:
148
- ambiguous_char: N
149
- ambiguous_emission_prob: 0.25
150
- germline: T
151
- name: insert_left_T
152
- transitions:
153
- IGHD1-20_star_01_0: 0.014705882352941176
154
- IGHD1-20_star_01_1: 0.014705882352941176
155
- IGHD1-20_star_01_10: 0.014705882352941176
156
- IGHD1-20_star_01_11: 0.014705882352941176
157
- IGHD1-20_star_01_12: 0.014705882352941176
158
- IGHD1-20_star_01_13: 0.014705882352941176
159
- IGHD1-20_star_01_14: 0.014705882352941176
160
- IGHD1-20_star_01_15: 0.014705882352941176
161
- IGHD1-20_star_01_16: 0.014705882352941176
162
- IGHD1-20_star_01_2: 0.014705882352941176
163
- IGHD1-20_star_01_3: 0.029411764705882353
164
- IGHD1-20_star_01_4: 0.019607843137254905
165
- IGHD1-20_star_01_5: 0.009803921568627454
166
- IGHD1-20_star_01_6: 3.2653618371328133e-18
167
- IGHD1-20_star_01_7: 0.014705882352941176
168
- IGHD1-20_star_01_8: 0.014705882352941176
169
- IGHD1-20_star_01_9: 0.014705882352941176
170
- insert_left_A: 0.0851063829787234
171
- insert_left_C: 0.3404255319148936
172
- insert_left_G: 0.1223404255319149
173
- insert_left_T: 0.2021276595744681
174
- - !!python/object:python.hmmwriter.State
175
- emissions:
176
- probs:
177
- A: 0.03554276055302745
178
- C: 0.03554276055302745
179
- G: 0.8933717183409177
180
- T: 0.03554276055302745
181
- track: nukes
182
- extras:
183
- ambiguous_char: N
184
- ambiguous_emission_prob: 0.25
185
- germline: G
186
- name: IGHD1-20_star_01_0
187
- transitions:
188
- IGHD1-20_star_01_1: 0.9411764705882353
189
- end: 0.058823529411764705
190
- - !!python/object:python.hmmwriter.State
191
- emissions:
192
- probs:
193
- A: 0.035297268639728104
194
- C: 0.035297268639728104
195
- G: 0.8941081940808157
196
- T: 0.035297268639728104
197
- track: nukes
198
- extras:
199
- ambiguous_char: N
200
- ambiguous_emission_prob: 0.25
201
- germline: G
202
- name: IGHD1-20_star_01_1
203
- transitions:
204
- IGHD1-20_star_01_2: 0.9411764705882353
205
- end: 0.058823529411764705
206
- - !!python/object:python.hmmwriter.State
207
- emissions:
208
- probs:
209
- A: 0.035051776726428764
210
- C: 0.035051776726428764
211
- G: 0.035051776726428764
212
- T: 0.8948446698207138
213
- track: nukes
214
- extras:
215
- ambiguous_char: N
216
- ambiguous_emission_prob: 0.25
217
- germline: T
218
- name: IGHD1-20_star_01_2
219
- transitions:
220
- IGHD1-20_star_01_3: 0.9411764705882353
221
- end: 0.058823529411764705
222
- - !!python/object:python.hmmwriter.State
223
- emissions:
224
- probs:
225
- A: 0.8908861127187617
226
- C: 0.036371295760412745
227
- G: 0.036371295760412745
228
- T: 0.036371295760412745
229
- track: nukes
230
- extras:
231
- ambiguous_char: N
232
- ambiguous_emission_prob: 0.25
233
- germline: A
234
- name: IGHD1-20_star_01_3
235
- transitions:
236
- IGHD1-20_star_01_4: 0.9411764705882353
237
- end: 0.058823529411764705
238
- - !!python/object:python.hmmwriter.State
239
- emissions:
240
- probs:
241
- A: 0.036647474162874505
242
- C: 0.036647474162874505
243
- G: 0.036647474162874505
244
- T: 0.8900575775113765
245
- track: nukes
246
- extras:
247
- ambiguous_char: N
248
- ambiguous_emission_prob: 0.25
249
- germline: T
250
- name: IGHD1-20_star_01_4
251
- transitions:
252
- IGHD1-20_star_01_5: 1.0
253
- - !!python/object:python.hmmwriter.State
254
- emissions:
255
- probs:
256
- A: 0.8892290423039911
257
- C: 0.03692365256533627
258
- G: 0.03692365256533627
259
- T: 0.03692365256533627
260
- track: nukes
261
- extras:
262
- ambiguous_char: N
263
- ambiguous_emission_prob: 0.25
264
- germline: A
265
- name: IGHD1-20_star_01_5
266
- transitions:
267
- IGHD1-20_star_01_6: 0.9803921568627451
268
- end: 0.01960784313725492
269
- - !!python/object:python.hmmwriter.State
270
- emissions:
271
- probs:
272
- A: 0.8884005070966059
273
- C: 0.03719983096779804
274
- G: 0.03719983096779804
275
- T: 0.03719983096779804
276
- track: nukes
277
- extras:
278
- ambiguous_char: N
279
- ambiguous_emission_prob: 0.25
280
- germline: A
281
- name: IGHD1-20_star_01_6
282
- transitions:
283
- IGHD1-20_star_01_7: 0.9607843137254902
284
- end: 0.039215686274509824
285
- - !!python/object:python.hmmwriter.State
286
- emissions:
287
- probs:
288
- A: 0.0374760093702598
289
- C: 0.8875719718892205
290
- G: 0.0374760093702598
291
- T: 0.0374760093702598
292
- track: nukes
293
- extras:
294
- ambiguous_char: N
295
- ambiguous_emission_prob: 0.25
296
- germline: C
297
- name: IGHD1-20_star_01_7
298
- transitions:
299
- IGHD1-20_star_01_8: 0.9411764705882353
300
- end: 0.05882352941176472
301
- - !!python/object:python.hmmwriter.State
302
- emissions:
303
- probs:
304
- A: 0.03750669585942222
305
- C: 0.03750669585942222
306
- G: 0.03750669585942222
307
- T: 0.8874799124217333
308
- track: nukes
309
- extras:
310
- ambiguous_char: N
311
- ambiguous_emission_prob: 0.25
312
- germline: T
313
- name: IGHD1-20_star_01_8
314
- transitions:
315
- IGHD1-20_star_01_9: 0.9215686274509803
316
- end: 0.07843137254901962
317
- - !!python/object:python.hmmwriter.State
318
- emissions:
319
- probs:
320
- A: 0.0374760093702598
321
- C: 0.0374760093702598
322
- G: 0.8875719718892205
323
- T: 0.0374760093702598
324
- track: nukes
325
- extras:
326
- ambiguous_char: N
327
- ambiguous_emission_prob: 0.25
328
- germline: G
329
- name: IGHD1-20_star_01_9
330
- transitions:
331
- IGHD1-20_star_01_10: 0.9019607843137255
332
- end: 0.09803921568627451
333
- - !!python/object:python.hmmwriter.State
334
- emissions:
335
- probs:
336
- A: 0.03719983096779804
337
- C: 0.03719983096779804
338
- G: 0.8884005070966059
339
- T: 0.03719983096779804
340
- track: nukes
341
- extras:
342
- ambiguous_char: N
343
- ambiguous_emission_prob: 0.25
344
- germline: G
345
- name: IGHD1-20_star_01_10
346
- transitions:
347
- IGHD1-20_star_01_11: 0.8823529411764706
348
- end: 0.11764705882352941
349
- - !!python/object:python.hmmwriter.State
350
- emissions:
351
- probs:
352
- A: 0.8970540970404078
353
- C: 0.03431530098653072
354
- G: 0.03431530098653072
355
- T: 0.03431530098653072
356
- track: nukes
357
- extras:
358
- ambiguous_char: N
359
- ambiguous_emission_prob: 0.25
360
- germline: A
361
- name: IGHD1-20_star_01_11
362
- transitions:
363
- IGHD1-20_star_01_12: 0.9411764705882353
364
- end: 0.058823529411764705
365
- - !!python/object:python.hmmwriter.State
366
- emissions:
367
- probs:
368
- A: 0.8963176213005097
369
- C: 0.034560792899830065
370
- G: 0.034560792899830065
371
- T: 0.034560792899830065
372
- track: nukes
373
- extras:
374
- ambiguous_char: N
375
- ambiguous_emission_prob: 0.25
376
- germline: A
377
- name: IGHD1-20_star_01_12
378
- transitions:
379
- IGHD1-20_star_01_13: 0.9411764705882353
380
- end: 0.058823529411764705
381
- - !!python/object:python.hmmwriter.State
382
- emissions:
383
- probs:
384
- A: 0.03480628481312942
385
- C: 0.8955811455606117
386
- G: 0.03480628481312942
387
- T: 0.03480628481312942
388
- track: nukes
389
- extras:
390
- ambiguous_char: N
391
- ambiguous_emission_prob: 0.25
392
- germline: C
393
- name: IGHD1-20_star_01_13
394
- transitions:
395
- IGHD1-20_star_01_14: 0.9411764705882353
396
- end: 0.058823529411764705
397
- - !!python/object:python.hmmwriter.State
398
- emissions:
399
- probs:
400
- A: 0.035051776726428764
401
- C: 0.035051776726428764
402
- G: 0.8948446698207138
403
- T: 0.035051776726428764
404
- track: nukes
405
- extras:
406
- ambiguous_char: N
407
- ambiguous_emission_prob: 0.25
408
- germline: G
409
- name: IGHD1-20_star_01_14
410
- transitions:
411
- IGHD1-20_star_01_15: 0.9411764705882353
412
- end: 0.058823529411764705
413
- - !!python/object:python.hmmwriter.State
414
- emissions:
415
- probs:
416
- A: 0.8941081940808157
417
- C: 0.035297268639728104
418
- G: 0.035297268639728104
419
- T: 0.035297268639728104
420
- track: nukes
421
- extras:
422
- ambiguous_char: N
423
- ambiguous_emission_prob: 0.25
424
- germline: A
425
- name: IGHD1-20_star_01_15
426
- transitions:
427
- IGHD1-20_star_01_16: 0.9411764705882353
428
- end: 0.058823529411764705
429
- - !!python/object:python.hmmwriter.State
430
- emissions:
431
- probs:
432
- A: 0.03554276055302745
433
- C: 0.8933717183409177
434
- G: 0.03554276055302745
435
- T: 0.03554276055302745
436
- track: nukes
437
- extras:
438
- ambiguous_char: N
439
- ambiguous_emission_prob: 0.25
440
- germline: C
441
- name: IGHD1-20_star_01_16
442
- transitions:
443
- end: 1.0
444
- tracks:
445
- nukes:
446
- - A
447
- - C
448
- - G
449
- - T