pg-sui 0.2.0__py3-none-any.whl → 1.6.14.dev9__py3-none-any.whl

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Files changed (127) hide show
  1. {pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info}/METADATA +101 -79
  2. pg_sui-1.6.14.dev9.dist-info/RECORD +81 -0
  3. {pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info}/WHEEL +1 -1
  4. pg_sui-1.6.14.dev9.dist-info/entry_points.txt +4 -0
  5. {pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info/licenses}/LICENSE +0 -0
  6. pg_sui-1.6.14.dev9.dist-info/top_level.txt +1 -0
  7. pgsui/__init__.py +35 -54
  8. pgsui/_version.py +34 -0
  9. pgsui/cli.py +909 -0
  10. pgsui/data_processing/__init__.py +0 -0
  11. pgsui/data_processing/config.py +565 -0
  12. pgsui/data_processing/containers.py +1424 -0
  13. pgsui/data_processing/transformers.py +557 -907
  14. pgsui/{example_data/trees → electron/app}/__init__.py +0 -0
  15. pgsui/electron/app/__main__.py +5 -0
  16. pgsui/electron/app/extra-resources/.gitkeep +1 -0
  17. pgsui/electron/app/icons/icons/1024x1024.png +0 -0
  18. pgsui/electron/app/icons/icons/128x128.png +0 -0
  19. pgsui/electron/app/icons/icons/16x16.png +0 -0
  20. pgsui/electron/app/icons/icons/24x24.png +0 -0
  21. pgsui/electron/app/icons/icons/256x256.png +0 -0
  22. pgsui/electron/app/icons/icons/32x32.png +0 -0
  23. pgsui/electron/app/icons/icons/48x48.png +0 -0
  24. pgsui/electron/app/icons/icons/512x512.png +0 -0
  25. pgsui/electron/app/icons/icons/64x64.png +0 -0
  26. pgsui/electron/app/icons/icons/icon.icns +0 -0
  27. pgsui/electron/app/icons/icons/icon.ico +0 -0
  28. pgsui/electron/app/main.js +227 -0
  29. pgsui/electron/app/package-lock.json +6894 -0
  30. pgsui/electron/app/package.json +51 -0
  31. pgsui/electron/app/preload.js +15 -0
  32. pgsui/electron/app/server.py +157 -0
  33. pgsui/electron/app/ui/logo.png +0 -0
  34. pgsui/electron/app/ui/renderer.js +131 -0
  35. pgsui/electron/app/ui/styles.css +59 -0
  36. pgsui/electron/app/ui/ui_shim.js +72 -0
  37. pgsui/electron/bootstrap.py +43 -0
  38. pgsui/electron/launch.py +57 -0
  39. pgsui/electron/package.json +14 -0
  40. pgsui/example_data/__init__.py +0 -0
  41. pgsui/example_data/phylip_files/__init__.py +0 -0
  42. pgsui/example_data/phylip_files/test.phy +0 -0
  43. pgsui/example_data/popmaps/__init__.py +0 -0
  44. pgsui/example_data/popmaps/{test.popmap → phylogen_nomx.popmap} +185 -99
  45. pgsui/example_data/structure_files/__init__.py +0 -0
  46. pgsui/example_data/structure_files/test.pops.2row.allsites.str +0 -0
  47. pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz +0 -0
  48. pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi +0 -0
  49. pgsui/impute/__init__.py +0 -0
  50. pgsui/impute/deterministic/imputers/allele_freq.py +725 -0
  51. pgsui/impute/deterministic/imputers/mode.py +844 -0
  52. pgsui/impute/deterministic/imputers/nmf.py +221 -0
  53. pgsui/impute/deterministic/imputers/phylo.py +973 -0
  54. pgsui/impute/deterministic/imputers/ref_allele.py +669 -0
  55. pgsui/impute/supervised/__init__.py +0 -0
  56. pgsui/impute/supervised/base.py +343 -0
  57. pgsui/impute/{unsupervised/models/in_development → supervised/imputers}/__init__.py +0 -0
  58. pgsui/impute/supervised/imputers/hist_gradient_boosting.py +317 -0
  59. pgsui/impute/supervised/imputers/random_forest.py +291 -0
  60. pgsui/impute/unsupervised/__init__.py +0 -0
  61. pgsui/impute/unsupervised/base.py +1118 -0
  62. pgsui/impute/unsupervised/callbacks.py +92 -262
  63. {simulation → pgsui/impute/unsupervised/imputers}/__init__.py +0 -0
  64. pgsui/impute/unsupervised/imputers/autoencoder.py +1285 -0
  65. pgsui/impute/unsupervised/imputers/nlpca.py +1554 -0
  66. pgsui/impute/unsupervised/imputers/ubp.py +1575 -0
  67. pgsui/impute/unsupervised/imputers/vae.py +1228 -0
  68. pgsui/impute/unsupervised/loss_functions.py +261 -0
  69. pgsui/impute/unsupervised/models/__init__.py +0 -0
  70. pgsui/impute/unsupervised/models/autoencoder_model.py +215 -567
  71. pgsui/impute/unsupervised/models/nlpca_model.py +155 -394
  72. pgsui/impute/unsupervised/models/ubp_model.py +180 -1106
  73. pgsui/impute/unsupervised/models/vae_model.py +269 -630
  74. pgsui/impute/unsupervised/nn_scorers.py +255 -0
  75. pgsui/utils/__init__.py +0 -0
  76. pgsui/utils/classification_viz.py +608 -0
  77. pgsui/utils/logging_utils.py +22 -0
  78. pgsui/utils/misc.py +35 -480
  79. pgsui/utils/plotting.py +996 -829
  80. pgsui/utils/pretty_metrics.py +290 -0
  81. pgsui/utils/scorers.py +213 -666
  82. pg_sui-0.2.0.dist-info/RECORD +0 -75
  83. pg_sui-0.2.0.dist-info/top_level.txt +0 -3
  84. pgsui/example_data/phylip_files/test_n10.phy +0 -118
  85. pgsui/example_data/phylip_files/test_n100.phy +0 -118
  86. pgsui/example_data/phylip_files/test_n2.phy +0 -118
  87. pgsui/example_data/phylip_files/test_n500.phy +0 -118
  88. pgsui/example_data/structure_files/test.nopops.1row.10sites.str +0 -117
  89. pgsui/example_data/structure_files/test.nopops.2row.100sites.str +0 -234
  90. pgsui/example_data/structure_files/test.nopops.2row.10sites.str +0 -234
  91. pgsui/example_data/structure_files/test.nopops.2row.30sites.str +0 -234
  92. pgsui/example_data/structure_files/test.nopops.2row.allsites.str +0 -234
  93. pgsui/example_data/structure_files/test.pops.1row.10sites.str +0 -117
  94. pgsui/example_data/structure_files/test.pops.2row.10sites.str +0 -234
  95. pgsui/example_data/trees/test.iqtree +0 -376
  96. pgsui/example_data/trees/test.qmat +0 -5
  97. pgsui/example_data/trees/test.rate +0 -2033
  98. pgsui/example_data/trees/test.tre +0 -1
  99. pgsui/example_data/trees/test_n10.rate +0 -19
  100. pgsui/example_data/trees/test_n100.rate +0 -109
  101. pgsui/example_data/trees/test_n500.rate +0 -509
  102. pgsui/example_data/trees/test_siterates.txt +0 -2024
  103. pgsui/example_data/trees/test_siterates_n10.txt +0 -10
  104. pgsui/example_data/trees/test_siterates_n100.txt +0 -100
  105. pgsui/example_data/trees/test_siterates_n500.txt +0 -500
  106. pgsui/example_data/vcf_files/test.vcf +0 -244
  107. pgsui/example_data/vcf_files/test.vcf.gz +0 -0
  108. pgsui/example_data/vcf_files/test.vcf.gz.tbi +0 -0
  109. pgsui/impute/estimators.py +0 -1268
  110. pgsui/impute/impute.py +0 -1463
  111. pgsui/impute/simple_imputers.py +0 -1431
  112. pgsui/impute/supervised/iterative_imputer_fixedparams.py +0 -782
  113. pgsui/impute/supervised/iterative_imputer_gridsearch.py +0 -1024
  114. pgsui/impute/unsupervised/keras_classifiers.py +0 -697
  115. pgsui/impute/unsupervised/models/in_development/cnn_model.py +0 -486
  116. pgsui/impute/unsupervised/neural_network_imputers.py +0 -1440
  117. pgsui/impute/unsupervised/neural_network_methods.py +0 -1395
  118. pgsui/pg_sui.py +0 -261
  119. pgsui/utils/sequence_tools.py +0 -407
  120. simulation/sim_benchmarks.py +0 -333
  121. simulation/sim_treeparams.py +0 -475
  122. test/__init__.py +0 -0
  123. test/pg_sui_simtest.py +0 -215
  124. test/pg_sui_testing.py +0 -523
  125. test/test.py +0 -151
  126. test/test_pgsui.py +0 -374
  127. test/test_tkc.py +0 -185
pgsui/example_data/vcf_files/test.vcf DELETED
@@ -1,244 +0,0 @@
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- ##fileformat=VCFv4.0
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- ##fileDate=2018/12/24
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- ##source=ipyrad_v.0.7.28
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- ##reference=GCF_002925995.2_T_m_triunguis-2.0_rna.fna
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- ##phasing=unphased
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- ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
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- ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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- ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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- ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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- ##FORMAT=<ID=CATG,Number=1,Type=String,Description="Base Counts (CATG)">
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- #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EAAL_BX1380 EAAL_BX1387 EAAL_BX211 EAAL_BXEA27 EAGA_BX217 EAGA_BX219 EAGA_BX220 EAGA_BX301 EAGA_BX346 EAGA_BX472 EAGA_BX473 EAGA_BX660 EAGA_BXEA14 EAGA_BXEA15_654 EAGA_BXEA17 EAGA_BXEA19 EAGA_BXEA21 EAGA_BXEA25 EAGA_BXEA26 EAGA_BXEA29_655 EAGA_BXEA31_659 EAGA_BXEA32_662 EAGA_BXEA33_663 EAGA_BXEA34_665 EAGA_BXEA35_666 EAGA_BXEA49_564 EAKY_BX26 EAKY_BX27 EANC_BX316 EANC_BX318 EANY_BXEA11 EAPA_BXEA13 EASC_BX1108 EASC_BX1109 EASC_BX1110 EASC_BX1111 EASC_BX1112 EASC_BX1114 EASC_BX1115 EASC_BX1116 EASC_BX231 EASC_BX232 EASC_BXEA40_1304 EASC_BXEA41_1305 EASC_BXEA42_1306 EASC_BXEA43_1307 EATN_BX35 EATN_BXEA02_36x2 EAVA_BX101 EAVA_BX103 EAVA_BX104 EAVA_BX320 EAVA_BX321 EAWV_BX449 TCAL_BX1618 TCAL_BX271 TCAL_BX272 TCAL_BX273 TCAL_BX279 TCAL_BX280 TCAL_BX281 TCAL_BX289 TCAL_BX302 TCGA_BX276 TCGA_BX300 TCGA_BX343 TCGA_BX344 TCGA_BX345 TCGA_BX589 TCGA_BXTC34 TCGA_BXTC35 TCGA_BXTC36 TCGA_BXTC46 TTAR_BX507 TTAR_BX984 TTAR_BX987 TTKS_BXTT20_78 TTKS_BXTT23_132 TTLA_BX421 TTLA_BX422 TTLA_BX775 TTLA_BXTT13 TTLA_BXTT34_1482 TTLA_BXTT35_1486 TTLA_BXTT36_1491 TTLA_BXTT37_1492 TTLA_BXTT38_1493 TTLA_BXTT39_1498 TTMS_BX243 TTTX_BX11 TTTX_BX15 TTTX_BX16 TTTX_BX19 TTTX_BX22 TTTX_BX222 TTTX_BX223 TTTX_BX224 TTTX_BX225 TTTX_BX227 TTTX_BX228 TTTX_BX23
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- XM_024192520.2 889 . T C 13 PASS . GT:DP:CATG ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/0:29:0,0,29,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/0:6:0,0,6,0 0/0:75:1,0,74,0 0/0:68:0,0,68,0 0/0:34:0,0,34,0 ./.:0:0,0,0,0 0/0:81:0,0,81,0 ./.:0:0,0,0,0 0/0:54:0,0,54,0 0/0:56:0,0,56,0 0/0:33:0,0,33,0 0/0:35:0,0,35,0 0/0:21:0,0,21,0 0/0:25:0,0,25,0 0/0:9:0,0,9,0 0/0:85:0,0,85,0 0/0:95:0,0,95,0 0/0:92:0,0,92,0 0/0:98:0,0,98,0 0/0:82:0,0,82,0 0/0:60:0,0,60,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/1:120:53,0,67,0 0/0:14:0,0,14,0 0/0:58:0,0,58,0 0/0:48:0,0,48,0 0/0:157:0,0,157,0 0/0:49:0,0,49,0 0/0:20:0,0,20,0 0/0:18:0,0,18,0 0/0:57:0,0,57,0 0/0:12:0,0,12,0 0/0:96:0,0,96,0 0/0:71:0,0,71,0 0/0:60:0,0,60,0 0/0:74:0,0,74,0 ./.:0:0,0,0,0 0/0:13:0,0,13,0 0/0:122:0,0,122,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/0:152:0,0,152,0 0/0:107:0,0,107,0 ./.:0:0,0,0,0 0/0:13:0,0,13,0 0/0:15:0,0,15,0 0/0:14:1,0,13,0 0/0:24:0,0,24,0 0/0:32:0,0,32,0 0/0:17:0,0,17,0 0/0:12:0,0,12,0 0/0:15:0,0,15,0 0/0:45:0,0,45,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/0:26:0,0,26,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/0:41:0,0,41,0 0/0:23:0,0,23,0 0/0:29:0,0,29,0 ./.:0:0,0,0,0 0/0:47:0,0,47,0 0/1:20:8,0,12,0 0/0:27:0,0,27,0 0/0:157:0,0,157,0 0/0:59:0,0,59,0 0/1:22:18,0,4,0 0/1:31:12,0,19,0 ./.:0:0,0,0,0 0/1:22:14,0,8,0 0/0:37:0,0,37,0 0/1:80:39,0,41,0 0/0:126:0,0,126,0 0/0:234:0,0,234,0 0/0:96:0,0,96,0 0/1:279:138,0,141,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 0/1:130:62,0,68,0 0/0:180:0,0,180,0 ./.:0:0,0,0,0 0/0:141:0,0,141,0 0/0:83:0,0,83,0 0/1:102:49,0,53,0 ./.:0:0,0,0,0
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