pg-sui 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl

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  1. {pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/METADATA +51 -70
  2. pg_sui-1.6.8.dist-info/RECORD +78 -0
  3. {pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/WHEEL +1 -1
  4. pg_sui-1.6.8.dist-info/entry_points.txt +4 -0
  5. pg_sui-1.6.8.dist-info/top_level.txt +1 -0
  6. pgsui/__init__.py +35 -54
  7. pgsui/_version.py +34 -0
  8. pgsui/cli.py +635 -0
  9. pgsui/data_processing/config.py +576 -0
  10. pgsui/data_processing/containers.py +1782 -0
  11. pgsui/data_processing/transformers.py +121 -1103
  12. pgsui/electron/app/__main__.py +5 -0
  13. pgsui/electron/app/icons/icons/1024x1024.png +0 -0
  14. pgsui/electron/app/icons/icons/128x128.png +0 -0
  15. pgsui/electron/app/icons/icons/16x16.png +0 -0
  16. pgsui/electron/app/icons/icons/24x24.png +0 -0
  17. pgsui/electron/app/icons/icons/256x256.png +0 -0
  18. pgsui/electron/app/icons/icons/32x32.png +0 -0
  19. pgsui/electron/app/icons/icons/48x48.png +0 -0
  20. pgsui/electron/app/icons/icons/512x512.png +0 -0
  21. pgsui/electron/app/icons/icons/64x64.png +0 -0
  22. pgsui/electron/app/icons/icons/icon.icns +0 -0
  23. pgsui/electron/app/icons/icons/icon.ico +0 -0
  24. pgsui/electron/app/main.js +189 -0
  25. pgsui/electron/app/package-lock.json +6893 -0
  26. pgsui/electron/app/package.json +50 -0
  27. pgsui/electron/app/preload.js +15 -0
  28. pgsui/electron/app/server.py +146 -0
  29. pgsui/electron/app/ui/logo.png +0 -0
  30. pgsui/electron/app/ui/renderer.js +130 -0
  31. pgsui/electron/app/ui/styles.css +59 -0
  32. pgsui/electron/app/ui/ui_shim.js +72 -0
  33. pgsui/electron/bootstrap.py +43 -0
  34. pgsui/electron/launch.py +59 -0
  35. pgsui/electron/package.json +14 -0
  36. pgsui/example_data/popmaps/{test.popmap → phylogen_nomx.popmap} +185 -99
  37. pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz +0 -0
  38. pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi +0 -0
  39. pgsui/impute/deterministic/imputers/allele_freq.py +691 -0
  40. pgsui/impute/deterministic/imputers/mode.py +679 -0
  41. pgsui/impute/deterministic/imputers/nmf.py +221 -0
  42. pgsui/impute/deterministic/imputers/phylo.py +971 -0
  43. pgsui/impute/deterministic/imputers/ref_allele.py +530 -0
  44. pgsui/impute/supervised/base.py +339 -0
  45. pgsui/impute/supervised/imputers/hist_gradient_boosting.py +293 -0
  46. pgsui/impute/supervised/imputers/random_forest.py +287 -0
  47. pgsui/impute/unsupervised/base.py +924 -0
  48. pgsui/impute/unsupervised/callbacks.py +89 -263
  49. pgsui/impute/unsupervised/imputers/autoencoder.py +972 -0
  50. pgsui/impute/unsupervised/imputers/nlpca.py +1264 -0
  51. pgsui/impute/unsupervised/imputers/ubp.py +1288 -0
  52. pgsui/impute/unsupervised/imputers/vae.py +957 -0
  53. pgsui/impute/unsupervised/loss_functions.py +158 -0
  54. pgsui/impute/unsupervised/models/autoencoder_model.py +208 -558
  55. pgsui/impute/unsupervised/models/nlpca_model.py +149 -468
  56. pgsui/impute/unsupervised/models/ubp_model.py +198 -1317
  57. pgsui/impute/unsupervised/models/vae_model.py +259 -618
  58. pgsui/impute/unsupervised/nn_scorers.py +215 -0
  59. pgsui/utils/classification_viz.py +591 -0
  60. pgsui/utils/misc.py +35 -480
  61. pgsui/utils/plotting.py +514 -824
  62. pgsui/utils/scorers.py +212 -438
  63. pg_sui-1.0.2.1.dist-info/RECORD +0 -75
  64. pg_sui-1.0.2.1.dist-info/top_level.txt +0 -3
  65. pgsui/example_data/phylip_files/test_n10.phy +0 -118
  66. pgsui/example_data/phylip_files/test_n100.phy +0 -118
  67. pgsui/example_data/phylip_files/test_n2.phy +0 -118
  68. pgsui/example_data/phylip_files/test_n500.phy +0 -118
  69. pgsui/example_data/structure_files/test.nopops.1row.10sites.str +0 -117
  70. pgsui/example_data/structure_files/test.nopops.2row.100sites.str +0 -234
  71. pgsui/example_data/structure_files/test.nopops.2row.10sites.str +0 -234
  72. pgsui/example_data/structure_files/test.nopops.2row.30sites.str +0 -234
  73. pgsui/example_data/structure_files/test.nopops.2row.allsites.str +0 -234
  74. pgsui/example_data/structure_files/test.pops.1row.10sites.str +0 -117
  75. pgsui/example_data/structure_files/test.pops.2row.10sites.str +0 -234
  76. pgsui/example_data/trees/test.iqtree +0 -376
  77. pgsui/example_data/trees/test.qmat +0 -5
  78. pgsui/example_data/trees/test.rate +0 -2033
  79. pgsui/example_data/trees/test.tre +0 -1
  80. pgsui/example_data/trees/test_n10.rate +0 -19
  81. pgsui/example_data/trees/test_n100.rate +0 -109
  82. pgsui/example_data/trees/test_n500.rate +0 -509
  83. pgsui/example_data/trees/test_siterates.txt +0 -2024
  84. pgsui/example_data/trees/test_siterates_n10.txt +0 -10
  85. pgsui/example_data/trees/test_siterates_n100.txt +0 -100
  86. pgsui/example_data/trees/test_siterates_n500.txt +0 -500
  87. pgsui/example_data/vcf_files/test.vcf +0 -244
  88. pgsui/example_data/vcf_files/test.vcf.gz +0 -0
  89. pgsui/example_data/vcf_files/test.vcf.gz.tbi +0 -0
  90. pgsui/impute/estimators.py +0 -735
  91. pgsui/impute/impute.py +0 -1486
  92. pgsui/impute/simple_imputers.py +0 -1439
  93. pgsui/impute/supervised/iterative_imputer_fixedparams.py +0 -785
  94. pgsui/impute/supervised/iterative_imputer_gridsearch.py +0 -1027
  95. pgsui/impute/unsupervised/keras_classifiers.py +0 -702
  96. pgsui/impute/unsupervised/models/in_development/cnn_model.py +0 -486
  97. pgsui/impute/unsupervised/neural_network_imputers.py +0 -1424
  98. pgsui/impute/unsupervised/neural_network_methods.py +0 -1549
  99. pgsui/pg_sui.py +0 -261
  100. pgsui/utils/sequence_tools.py +0 -407
  101. simulation/sim_benchmarks.py +0 -333
  102. simulation/sim_treeparams.py +0 -475
  103. test/__init__.py +0 -0
  104. test/pg_sui_simtest.py +0 -215
  105. test/pg_sui_testing.py +0 -523
  106. test/test.py +0 -297
  107. test/test_pgsui.py +0 -374
  108. test/test_tkc.py +0 -214
  109. {pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info/licenses}/LICENSE +0 -0
  110. /pgsui/{example_data/trees → electron/app}/__init__.py +0 -0
  111. /pgsui/impute/{unsupervised/models/in_development → supervised/imputers}/__init__.py +0 -0
  112. {simulation → pgsui/impute/unsupervised/imputers}/__init__.py +0 -0
pgsui/example_data/trees/test.tre DELETED
@@ -1 +0,0 @@
1
- ((((FLFL_BXFL01:0.01094754,FLFL_BX683:0.008014238):0.03387017,(((((EASC_BXEA43_1307:0.0060994364,EAGA_BX472:0.012144771):0.0016504257,((((((EAGA_BXEA49_564:0.010372005,TCAL_BXTC93:0.0064979377):9.402507E-4,EAGA_BXEA34_665:0.004493265):0.0020628884,(EAVA_BX101:0.003439303,EAGA_BXEA33_663:0.006730099):7.785329E-4):0.0015684908,(EAVA_BX320:0.007959818,EAVA_BX321:2.0682E-6):0.007150269):8.494874E-4,(((((((EAGA_BX660:0.004119524,(EAGA_BXEA35_666:0.0098991515,(EASC_BX1110:0.011941433,EASC_BX1112:0.014752431):0.0035045708):0.0011201733):8.158576E-4,(EASC_BX1115:0.009404895,EAGA_BXEA15_654:0.0033351006):0.0010331823):0.0011512865,(EAGA_BX346:0.005297047,TCAL_BX273:0.0072824056):0.0013585262):8.889416E-4,((TCAL_BX612:0.0050125527,EASC_BXEA41_1305:0.0046849027):2.5252E-6,EAGA_BXEA25:0.008647807):0.001378543):2.9004E-6,EAGA_BXEA32_662:0.009391725):0.0013076814,((((EASC_BXEA42_1306:0.0099450955,TCAL_BXTC80:0.0045147077):7.598317E-4,(EASC_BX1109:0.0032225691,TCGA_BX344:0.0051967893):0.0022761857):0.0031016914,TCAL_BX279:0.007073297):2.7583E-6,EATN_BXEA02_36x2:0.008299036):0.0011600876):0.0015647858,((EAAL_BXEA27:0.009142484,EAGA_BXEA31_659:0.004881493):0.0014022489,EAGA_BX301:0.010543813):7.256198E-4):0.0018600221):7.867081E-4,(EASC_BXEA40_1304:0.0035972318,TCAL_BXTC110:0.0048929085):0.0024339203):0.001164745):0.0025087355,(EAGA_BXEA21:0.009535364,TCAL_BXTC92:0.008521069):2.1683E-6):0.0016246842,EASC_BX1108:0.01244127):0.0014236966,EASC_BX1114:0.01278142):0.0044297455):0.0015333567,(EAGA_BXEA17:6.66352E-4,((((TTLA_BXTT35_1486:0.011551925,TTTX_BX227:0.0076743416):0.0015495993,((((TTAR_BX507:0.011749585,TTLA_BXTT38_1493:0.00687887):0.0034069817,(((TTTX_BX225:0.00878936,TTLA_BXTT13:0.006902939):0.0014737586,TTLA_BXTT39_1498:0.009089908):2.1449E-6,TTAR_BX987:0.011556541):9.999461E-4):0.0020502205,(TTTX_BX222:0.009645971,TTAR_BX984:0.010388089):0.0021065176):0.0014258397,((TTLA_BXTT34_1482:0.0077409507,(TTLA_BXTT36_1491:0.0047578174,((TTLA_BXTT37_1492:0.009461152,TTTX_BX228:0.010235932):0.0011037224,TTTX_BX223:0.009745779):0.0011680451):4.575483E-4):6.271501E-4,(TTLA_BX421:0.0052830335,TTLA_BX422:0.0050254604):0.0018790524):0.0022438997):0.0014583132):0.004239977,(TTKS_BXTT20_78:0.0135013545,((MXMX_BX1195:0.0057988055,MXMX_BX1194:0.0063597243):0.0029546232,MXMX_BX1196:0.006797728):0.02399073):8.124931E-4):0.012514747,(TCAL_BXTC63:0.009390146,(GUMS_BXGU69_AA43:0.0024400593,((GUMS_BXGU49_T66:0.0052715335,GUMS_BXGU47_T61:0.0058908816):6.137743E-4,(((((((((GUMS_BXGU68_AA42:0.012788657,GUMS_BXGU67_AA41:0.0040612766):0.0022325697,(GUMS_BXGU50_T69:0.0050785327,GUMS_BXGU56_T83:0.009042775):0.0025575936):0.0022290286,GUMS_BXGU43_T55:0.0047226856):2.049E-6,GUMS_BXGU75_AA49:0.0069396426):0.0029005336,GUMS_BXGU58_T92:0.009175001):2.038E-6,GUMS_BX200:0.00983445):0.002292576,(CHCH_BX1191:0.0027365615,CHCH_BX1193:0.0021688642):0.020654544):6.618583E-4,(((GUMS_BXGU53_T72:0.004064852,GUMS_BXGU45_T59:0.0027521672):0.007975526,((((GUMS_BXGU78_AA52:0.0030857737,GUMS_BXGU77_AA51:0.0051228595):0.0045023,GUMS_BXGU74_AA48:0.0044523785):0.0018474367,((GUMS_BXGU76_AA50:0.009512262,GUMS_BXGU71_AA45:0.0069703814):0.001294317,GUMS_BXGU72_AA46:0.008265343):2.9501E-6):0.0017138595,((GUMS_BXGU73_AA47:0.0064422814,GUMS_BXGU54_T73:0.0062324773):0.004293427,GUMS_BXGU79_AA73:0.005225335):0.0030584936):0.0013961131):0.0019044699,GUMS_BXGU48_T62:0.004893909):0.0019652552):0.0011093861,(GUMS_BXGU44_T56:0.00373924,((GUFL_BX626:0.013016185,GUFL_BXGU62_AA36:0.004237289):0.0016172576,(GUFL_BX684:0.004644579,(GUFL_BXGU61_U57:0.0026708753,(GUFL_BXGU63_AA37:0.008784231,((((GUFL_BXGU65_AA39:0.0052446947,GUFL_BX685:0.0036272586):0.002929856,GUFL_BXGU35_AA13:0.008585323):2.0424E-6,GUFL_BX503:0.003015814):0.0016814033,(GUFL_BX504:0.0031465883,(GUFL_BXGU36_AA14:0.008493794,(GUFL_BXGU32:0.0051620225,GUFL_BXGU33:0.0050123283):0.0017017642):0.0021553873):0.002047458):3.442552E-4):0.0014695337):0.0026579886):0.0017915547):0.008358822):0.0013967645):0.0017900784):0.0029705653):0.0018421618):0.0024316788):2.6957E-6):9.188092E-4):0.08104106,((((DSAZ_BX1213:0.011834233,DSNM_BXDS02:0.0044685267):0.008568451,ONTX_BXON46_153:0.00906274):0.003856124,(((((((((ONWI_BX489:0.0038895435,(ONWI_BX491:0.0055481307,ONWI_BX490:0.00464839):0.0033254311):0.0026287122,ONWI_BX495:0.0027921735):0.004821467,(ONWI_BX493:0.0031390742,ONWI_BX497:0.0052997973):0.0032650298):0.0032805926,ONWI_BX486:0.0070235464):0.0054801693,ONNE_BXON58_433x2:0.0039076935):0.005021405,ONCO_BX601:0.007124628):0.0050125946,ONKS_BXON61_133:0.0056786947):0.001604562,(ONCO_BX580:0.0074652294,ONCO_BX602:0.008312122):9.276972E-4):0.004760113,ONTX_BXON45_150:0.009037679):9.465904E-4):0.0013552041,ONCO_BX588:0.008843728):0.01377698);
pgsui/example_data/trees/test_n10.rate DELETED
@@ -1,19 +0,0 @@
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- # Site-specific subtitution rates determined by empirical Bayesian method
2
- # This file can be read in MS Excel or in R with command:
3
- # tab=read.table('test.phy.rate',header=TRUE)
4
- # Columns are tab-separated with following meaning:
5
- # Site: Alignment site ID
6
- # Rate: Posterior mean site rate weighted by posterior probability
7
- # Cat: Category with highest posterior (0=invariable, 1=slow, etc)
8
- # C_Rate: Corresponding rate of highest category
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- Site Rate Cat C_Rate
10
- 1 0.65244 1 0.41526
11
- 2 0.71905 1 0.41526
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- 3 0.66729 1 0.41526
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- 4 2.65438 2 2.84311
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- 5 0.45287 1 0.41526
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- 6 0.70798 1 0.41526
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- 7 0.70532 1 0.41526
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- 8 0.43881 1 0.41526
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- 9 0.46221 1 0.41526
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- 10 0.69352 1 0.41526
pgsui/example_data/trees/test_n100.rate DELETED
@@ -1,109 +0,0 @@
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- # Site-specific subtitution rates determined by empirical Bayesian method
2
- # This file can be read in MS Excel or in R with command:
3
- # tab=read.table('test.phy.rate',header=TRUE)
4
- # Columns are tab-separated with following meaning:
5
- # Site: Alignment site ID
6
- # Rate: Posterior mean site rate weighted by posterior probability
7
- # Cat: Category with highest posterior (0=invariable, 1=slow, etc)
8
- # C_Rate: Corresponding rate of highest category
9
- Site Rate Cat C_Rate
10
- 1 0.65244 1 0.41526
11
- 2 0.71905 1 0.41526
12
- 3 0.66729 1 0.41526
13
- 4 2.65438 2 2.84311
14
- 5 0.45287 1 0.41526
15
- 6 0.70798 1 0.41526
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- 7 0.70532 1 0.41526
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- 8 0.43881 1 0.41526
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- 9 0.46221 1 0.41526
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- 10 0.69352 1 0.41526
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- 11 0.72661 1 0.41526
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- 12 0.59677 1 0.41526
22
- 13 0.45332 1 0.41526
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- 14 0.45439 1 0.41526
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- 15 0.58785 1 0.41526
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- 16 0.41904 1 0.41526
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- 17 0.41957 1 0.41526
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- 18 0.45609 1 0.41526
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- 19 0.46272 1 0.41526
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- 20 2.78146 2 2.84311
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- 21 0.46007 1 0.41526
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- 22 3.10141 2 2.84311
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- 23 0.65251 1 0.41526
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- 24 0.41980 1 0.41526
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- 25 0.45148 1 0.41526
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- 26 0.42018 1 0.41526
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- 27 0.46300 1 0.41526
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- 28 0.41985 1 0.41526
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- 29 0.45384 1 0.41526
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- 30 0.64632 1 0.41526
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- 31 0.57909 1 0.41526
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- 32 0.45676 1 0.41526
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- 33 0.42065 1 0.41526
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- 34 11.38813 3 11.47065
44
- 35 0.57922 1 0.41526
45
- 36 0.41990 1 0.41526
46
- 37 0.45883 1 0.41526
47
- 38 0.46317 1 0.41526
48
- 39 0.42012 1 0.41526
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- 40 0.45216 1 0.41526
50
- 41 0.45919 1 0.41526
51
- 42 0.66636 1 0.41526
52
- 43 0.45845 1 0.41526
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- 44 0.46051 1 0.41526
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- 45 0.64517 1 0.41526
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- 46 0.42045 1 0.41526
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- 47 0.44030 1 0.41526
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- 48 0.46461 1 0.41526
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- 49 0.71732 1 0.41526
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- 50 0.59264 1 0.41526
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- 51 0.64693 1 0.41526
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- 52 0.66550 1 0.41526
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- 53 0.60314 1 0.41526
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- 54 0.43862 1 0.41526
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- 55 0.46164 1 0.41526
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- 56 0.44372 1 0.41526
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- 57 0.45332 1 0.41526
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- 58 0.72411 1 0.41526
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- 59 0.46146 1 0.41526
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- 60 0.46257 1 0.41526
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- 61 0.45963 1 0.41526
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- 62 0.41847 1 0.41526
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- 63 0.45515 1 0.41526
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- 64 0.45363 1 0.41526
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- 65 0.42010 1 0.41526
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- 66 0.46190 1 0.41526
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- 67 0.42011 1 0.41526
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- 68 0.45383 1 0.41526
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- 69 0.44188 1 0.41526
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- 70 0.41850 1 0.41526
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- 71 0.42156 1 0.41526
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- 72 0.45332 1 0.41526
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- 73 0.71182 1 0.41526
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- 74 0.42004 1 0.41526
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- 75 0.70672 1 0.41526
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- 76 0.69578 1 0.41526
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- 77 0.46186 1 0.41526
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- 78 0.72224 1 0.41526
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- 79 0.45927 1 0.41526
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- 80 0.41992 1 0.41526
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- 81 11.44929 3 11.47065
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- 82 0.45904 1 0.41526
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- 83 0.45993 1 0.41526
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- 84 0.66309 1 0.41526
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- 85 0.43970 1 0.41526
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- 86 0.42028 1 0.41526
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- 87 0.45349 1 0.41526
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- 88 0.41855 1 0.41526
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- 89 0.65589 1 0.41526
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- 90 0.42027 1 0.41526
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- 91 0.44487 1 0.41526
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- 92 0.45594 1 0.41526
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- 93 0.42031 1 0.41526
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- 94 0.41862 1 0.41526
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- 95 0.65846 1 0.41526
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- 96 0.46094 1 0.41526
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- 97 0.45931 1 0.41526
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- 98 11.47016 3 11.47065
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- 99 11.47059 3 11.47065
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- 100 0.41926 1 0.41526
pgsui/example_data/trees/test_n500.rate DELETED
@@ -1,509 +0,0 @@
1
- # Site-specific subtitution rates determined by empirical Bayesian method
2
- # This file can be read in MS Excel or in R with command:
3
- # tab=read.table('test.phy.rate',header=TRUE)
4
- # Columns are tab-separated with following meaning:
5
- # Site: Alignment site ID
6
- # Rate: Posterior mean site rate weighted by posterior probability
7
- # Cat: Category with highest posterior (0=invariable, 1=slow, etc)
8
- # C_Rate: Corresponding rate of highest category
9
- Site Rate Cat C_Rate
10
- 1 0.65244 1 0.41526
11
- 2 0.71905 1 0.41526
12
- 3 0.66729 1 0.41526
13
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270
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311
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312
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314
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315
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316
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318
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319
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320
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322
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326
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330
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331
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333
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334
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335
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336
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347
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349
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350
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351
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352
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353
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354
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356
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360
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362
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364
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365
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367
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368
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370
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378
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379
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380
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381
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382
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383
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384
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385
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386
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387
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388
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389
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390
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392
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393
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394
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395
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396
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398
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399
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400
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401
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402
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403
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405
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406
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410
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411
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412
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413
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414
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415
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416
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417
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420
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421
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422
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427
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432
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433
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436
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438
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439
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440
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441
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442
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443
- 434 0.69037 1 0.41526
444
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445
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447
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454
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455
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456
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457
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458
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459
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460
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463
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464
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465
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466
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467
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468
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469
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470
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471
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472
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473
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474
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475
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477
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478
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479
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480
- 471 0.45736 1 0.41526
481
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482
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483
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484
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485
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486
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487
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488
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489
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490
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491
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492
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493
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494
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495
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496
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497
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498
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499
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500
- 491 2.84631 2 2.84311
501
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502
- 493 0.45441 1 0.41526
503
- 494 0.46163 1 0.41526
504
- 495 0.45846 1 0.41526
505
- 496 0.42024 1 0.41526
506
- 497 0.67825 1 0.41526
507
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509
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