partis-bcr 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

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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/hmm/hmms/IGHV3-7_star_05.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  !!python/object:python.hmmwriter.HMM
2
2
  extras:
3
- gene_prob: 0.08333333333333333
4
- overall_mute_freq: 0.012499999999999999
3
+ gene_prob: 0.3
4
+ overall_mute_freq: 0.019000000000000003
5
5
  per_gene_mute_freq: 0.11724158590751857
6
6
  name: IGHV3-7_star_05
7
7
  states:
test/new-results/test/parameters/simu/hmm/j-mean-mute-freqs.csv CHANGED
@@ -1,12 +1,12 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -0.01,0.0,,0.0
3
- 0.0,0.5555555555555556,,0.12422599874998833
3
+ 0.0,0.2,,0.1414213562373095
4
4
  0.01,0.0,,0.0
5
- 0.02,0.2777777777777778,,0.08784104611578832
5
+ 0.02,0.4,,0.2
6
6
  0.03,0.0,,0.0
7
- 0.04,0.027777777777777776,,0.027777777777777776
8
- 0.05,0.1111111111111111,,0.05555555555555555
9
- 0.06,0.027777777777777776,,0.027777777777777776
7
+ 0.04,0.0,,0.0
8
+ 0.05,0.4,,0.2
9
+ 0.06,0.0,,0.0
10
10
  0.07,0.0,,0.0
11
11
  0.08,0.0,,0.0
12
12
  0.09,0.0,,0.0
test/new-results/test/parameters/simu/hmm/j-mean-n-muted.csv CHANGED
@@ -1,9 +1,9 @@
1
1
  bin_low_edge,contents,binlabel,error
2
2
  -1.5,0.0,,0.0
3
- -0.5,20.0,,4.47213595499958
4
- 0.5,10.0,,3.1622776601683795
5
- 1.5,5.0,,2.23606797749979
6
- 2.5,1.0,,1.0
3
+ -0.5,2.0,,1.4142135623730951
4
+ 0.5,4.0,,2.0
5
+ 1.5,4.0,,2.0
6
+ 2.5,0.0,,0.0
7
7
  3.5,0.0,,0.0
8
8
  4.5,0.0,,0.0
9
9
  5.5,0.0,,0.0
test/new-results/test/parameters/simu/hmm/j_gene-dj_insertion-probs.csv CHANGED
@@ -1,10 +1,3 @@
1
1
  dj_insertion,j_gene,count
2
- 19,IGHJ6*02,2
3
- 1,IGHJ4*02,13
4
- 7,IGHJ4*02,3
5
- 17,IGHJ6*02,1
6
- 6,IGHJ4*02,1
7
- 0,IGHJ1*01,7
8
- 5,IGHJ4*02,7
9
- 3,IGHJ4*02,1
10
- 7,IGHJ1*01,1
2
+ 19,IGHJ6*02,3
3
+ 1,IGHJ4*02,7
test/new-results/test/parameters/simu/hmm/j_gene-j_3p_del-probs.csv CHANGED
@@ -1,4 +1,3 @@
1
1
  j_3p_del,j_gene,count
2
2
  0,IGHJ6*02,3
3
- 0,IGHJ4*02,25
4
- 0,IGHJ1*01,8
3
+ 0,IGHJ4*02,7
test/new-results/test/parameters/simu/hmm/j_gene-j_5p_del-probs.csv CHANGED
@@ -1,8 +1,3 @@
1
1
  j_5p_del,j_gene,count
2
- 17,IGHJ6*02,2
3
- 8,IGHJ4*02,15
4
- 4,IGHJ4*02,2
5
- 15,IGHJ6*02,1
6
- 3,IGHJ1*01,7
7
- 5,IGHJ4*02,8
8
- 6,IGHJ1*01,1
2
+ 17,IGHJ6*02,3
3
+ 8,IGHJ4*02,7
test/new-results/test/parameters/simu/hmm/j_gene-probs.csv CHANGED
@@ -1,4 +1,3 @@
1
1
  j_gene,count
2
2
  IGHJ6*02,3
3
- IGHJ4*02,25
4
- IGHJ1*01,8
3
+ IGHJ4*02,7
test/new-results/test/parameters/simu/hmm/jf_insertion-probs.csv CHANGED
@@ -1,2 +1,2 @@
1
1
  jf_insertion,count
2
- 0,36
2
+ 0,10
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHD6-13_star_01.csv CHANGED
@@ -1,20 +1,17 @@
1
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
- 0,0.0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711
3
- 1,0.0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711
4
- 2,0.0,0.0,0.215128129105,0.0,0,0.0,0.215128129105,0.0,0,0.0,0.215128129105,1.0,9,0.8959584598407622,1.0,0.0,0,0.0,0.215128129105
5
- 3,0.0,0.0,0.116160652917,0.0,0,0.0,0.116160652917,0.0,0,0.0,0.116160652917,0.0,0,0.0,0.116160652917,1.0,19,0.9465508226401592,1.0
6
- 4,0.0,0.0,0.111029434192,1.0,20,0.9490299978737119,1.0,0.0,0,0.0,0.111029434192,0.0,0,0.0,0.111029434192,0.0,0,0.0,0.111029434192
7
- 5,0.0,0.0,0.111029434192,0.0,0,0.0,0.111029434192,0.0,0,0.0,0.111029434192,0.0,0,0.0,0.111029434192,1.0,20,0.9490299978737119,1.0
8
- 6,0.05,0.035045319187,0.146074753379,0.95,19,0.853925246621,0.964954680813,0.05,1,0.035045319187,0.146074753379,0.0,0,0.0,0.111029434192,0.0,0,0.0,0.111029434192
9
- 7,0.0,0.0,0.10201236649,0.0,0,0.0,0.10201236649,0.0,0,0.0,0.10201236649,1.0,22,0.9533570832170496,1.0,0.0,0,0.0,0.10201236649
10
- 8,0.13636363636363635,0.09440648801,0.238249350229,0.09090909090909091,2,0.06173849709,0.187544260831,0.8636363636363636,19,0.761750649771,0.90559351199,0.0,0,0.0,0.10201236649,0.045454545454545456,1,0.03197857928,0.13399094577
11
- 9,0.0,0.0,0.098030022138,1.0,23,0.9552563816905354,1.0,0.0,0,0.0,0.098030022138,0.0,0,0.0,0.098030022138,0.0,0,0.0,0.098030022138
12
- 10,0.0,0.0,0.098030022138,0.0,0,0.0,0.098030022138,0.0,0,0.0,0.098030022138,1.0,23,0.9552563816905354,1.0,0.0,0,0.0,0.098030022138
13
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15
  16,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
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  17,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
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test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ4_star_02.csv CHANGED
@@ -1,45 +1,41 @@
1
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
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16
+ 22,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
17
+ 23,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
18
+ 24,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
19
+ 25,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
20
+ 26,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
21
+ 27,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
22
+ 28,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
23
+ 29,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
24
+ 30,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
25
+ 31,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
26
+ 32,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
27
+ 33,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
28
+ 34,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
29
+ 35,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
30
+ 36,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
31
+ 37,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
32
+ 38,0.14285714285714285,0.093118673237,0.351673214562,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.8571428571428571,6,0.648326785438,0.906881326763,0.14285714285714285,1,0.093118673237,0.351673214562
33
+ 39,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
34
+ 40,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
35
+ 41,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
36
+ 42,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
37
+ 43,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
38
+ 44,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0
39
+ 45,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
40
+ 46,0.0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325
41
+ 47,0.0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,0.0,0,0.0,0.258554541325,1.0,7,0.8716855428717357,1.0,0.0,0,0.0,0.258554541325
test/new-results/test/parameters/simu/hmm/mute-freqs/IGHJ6_star_02.csv CHANGED
@@ -1,6 +1,4 @@
1
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
- 15,0.0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711
3
- 16,1.0,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711,0.0,0,0.0,0.504622638711,1.0,1,0.5773502691896258,1.0,0.0,0,0.0,0.504622638711
4
2
  17,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
5
3
  18,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0,0.0,0,0.0,0.420398101924
6
4
  19,0.0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,0.0,0,0.0,0.420398101924,1.0,3,0.7598356856515925,1.0