PyPI - pg-sui - Versions diffs - 0.2.3__py3-none-any.whl → 1.6.16a3__py3-none-any.whl - Mend

pg-sui 0.2.3py3-none-any.whl → 1.6.16a3py3-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 (128) hide show

pg_sui-1.6.16a3.dist-info/METADATA +292 -0
pg_sui-1.6.16a3.dist-info/RECORD +81 -0
{pg_sui-0.2.3.dist-info → pg_sui-1.6.16a3.dist-info}/WHEEL +1 -1
pg_sui-1.6.16a3.dist-info/entry_points.txt +4 -0
{pg_sui-0.2.3.dist-info → pg_sui-1.6.16a3.dist-info/licenses}/LICENSE +0 -0
pg_sui-1.6.16a3.dist-info/top_level.txt +1 -0
pgsui/__init__.py +35 -54
pgsui/_version.py +34 -0
pgsui/cli.py +922 -0
pgsui/data_processing/__init__.py +0 -0
pgsui/data_processing/config.py +565 -0
pgsui/data_processing/containers.py +1436 -0
pgsui/data_processing/transformers.py +557 -907
pgsui/{example_data/trees → electron/app}/__init__.py +0 -0
pgsui/electron/app/__main__.py +5 -0
pgsui/electron/app/extra-resources/.gitkeep +1 -0
pgsui/electron/app/icons/icons/1024x1024.png +0 -0
pgsui/electron/app/icons/icons/128x128.png +0 -0
pgsui/electron/app/icons/icons/16x16.png +0 -0
pgsui/electron/app/icons/icons/24x24.png +0 -0
pgsui/electron/app/icons/icons/256x256.png +0 -0
pgsui/electron/app/icons/icons/32x32.png +0 -0
pgsui/electron/app/icons/icons/48x48.png +0 -0
pgsui/electron/app/icons/icons/512x512.png +0 -0
pgsui/electron/app/icons/icons/64x64.png +0 -0
pgsui/electron/app/icons/icons/icon.icns +0 -0
pgsui/electron/app/icons/icons/icon.ico +0 -0
pgsui/electron/app/main.js +227 -0
pgsui/electron/app/package-lock.json +6894 -0
pgsui/electron/app/package.json +51 -0
pgsui/electron/app/preload.js +15 -0
pgsui/electron/app/server.py +157 -0
pgsui/electron/app/ui/logo.png +0 -0
pgsui/electron/app/ui/renderer.js +131 -0
pgsui/electron/app/ui/styles.css +59 -0
pgsui/electron/app/ui/ui_shim.js +72 -0
pgsui/electron/bootstrap.py +43 -0
pgsui/electron/launch.py +57 -0
pgsui/electron/package.json +14 -0
pgsui/example_data/__init__.py +0 -0
pgsui/example_data/phylip_files/__init__.py +0 -0
pgsui/example_data/phylip_files/test.phy +0 -0
pgsui/example_data/popmaps/__init__.py +0 -0
pgsui/example_data/popmaps/{test.popmap → phylogen_nomx.popmap} +185 -99
pgsui/example_data/structure_files/__init__.py +0 -0
pgsui/example_data/structure_files/test.pops.2row.allsites.str +0 -0
pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz +0 -0
pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi +0 -0
pgsui/impute/__init__.py +0 -0
pgsui/impute/deterministic/imputers/allele_freq.py +725 -0
pgsui/impute/deterministic/imputers/mode.py +844 -0
pgsui/impute/deterministic/imputers/nmf.py +221 -0
pgsui/impute/deterministic/imputers/phylo.py +973 -0
pgsui/impute/deterministic/imputers/ref_allele.py +669 -0
pgsui/impute/supervised/__init__.py +0 -0
pgsui/impute/supervised/base.py +343 -0
pgsui/impute/{unsupervised/models/in_development → supervised/imputers}/__init__.py +0 -0
pgsui/impute/supervised/imputers/hist_gradient_boosting.py +317 -0
pgsui/impute/supervised/imputers/random_forest.py +291 -0
pgsui/impute/unsupervised/__init__.py +0 -0
pgsui/impute/unsupervised/base.py +1121 -0
pgsui/impute/unsupervised/callbacks.py +92 -262
{simulation → pgsui/impute/unsupervised/imputers}/__init__.py +0 -0
pgsui/impute/unsupervised/imputers/autoencoder.py +1361 -0
pgsui/impute/unsupervised/imputers/nlpca.py +1666 -0
pgsui/impute/unsupervised/imputers/ubp.py +1660 -0
pgsui/impute/unsupervised/imputers/vae.py +1316 -0
pgsui/impute/unsupervised/loss_functions.py +261 -0
pgsui/impute/unsupervised/models/__init__.py +0 -0
pgsui/impute/unsupervised/models/autoencoder_model.py +215 -567
pgsui/impute/unsupervised/models/nlpca_model.py +155 -394
pgsui/impute/unsupervised/models/ubp_model.py +180 -1106
pgsui/impute/unsupervised/models/vae_model.py +269 -630
pgsui/impute/unsupervised/nn_scorers.py +255 -0
pgsui/utils/__init__.py +0 -0
pgsui/utils/classification_viz.py +608 -0
pgsui/utils/logging_utils.py +22 -0
pgsui/utils/misc.py +35 -480
pgsui/utils/plotting.py +996 -829
pgsui/utils/pretty_metrics.py +290 -0
pgsui/utils/scorers.py +213 -666
pg_sui-0.2.3.dist-info/METADATA +0 -322
pg_sui-0.2.3.dist-info/RECORD +0 -75
pg_sui-0.2.3.dist-info/top_level.txt +0 -3
pgsui/example_data/phylip_files/test_n10.phy +0 -118
pgsui/example_data/phylip_files/test_n100.phy +0 -118
pgsui/example_data/phylip_files/test_n2.phy +0 -118
pgsui/example_data/phylip_files/test_n500.phy +0 -118
pgsui/example_data/structure_files/test.nopops.1row.10sites.str +0 -117
pgsui/example_data/structure_files/test.nopops.2row.100sites.str +0 -234
pgsui/example_data/structure_files/test.nopops.2row.10sites.str +0 -234
pgsui/example_data/structure_files/test.nopops.2row.30sites.str +0 -234
pgsui/example_data/structure_files/test.nopops.2row.allsites.str +0 -234
pgsui/example_data/structure_files/test.pops.1row.10sites.str +0 -117
pgsui/example_data/structure_files/test.pops.2row.10sites.str +0 -234
pgsui/example_data/trees/test.iqtree +0 -376
pgsui/example_data/trees/test.qmat +0 -5
pgsui/example_data/trees/test.rate +0 -2033
pgsui/example_data/trees/test.tre +0 -1
pgsui/example_data/trees/test_n10.rate +0 -19
pgsui/example_data/trees/test_n100.rate +0 -109
pgsui/example_data/trees/test_n500.rate +0 -509
pgsui/example_data/trees/test_siterates.txt +0 -2024
pgsui/example_data/trees/test_siterates_n10.txt +0 -10
pgsui/example_data/trees/test_siterates_n100.txt +0 -100
pgsui/example_data/trees/test_siterates_n500.txt +0 -500
pgsui/example_data/vcf_files/test.vcf +0 -244
pgsui/example_data/vcf_files/test.vcf.gz +0 -0
pgsui/example_data/vcf_files/test.vcf.gz.tbi +0 -0
pgsui/impute/estimators.py +0 -1268
pgsui/impute/impute.py +0 -1463
pgsui/impute/simple_imputers.py +0 -1431
pgsui/impute/supervised/iterative_imputer_fixedparams.py +0 -782
pgsui/impute/supervised/iterative_imputer_gridsearch.py +0 -1024
pgsui/impute/unsupervised/keras_classifiers.py +0 -697
pgsui/impute/unsupervised/models/in_development/cnn_model.py +0 -486
pgsui/impute/unsupervised/neural_network_imputers.py +0 -1440
pgsui/impute/unsupervised/neural_network_methods.py +0 -1395
pgsui/pg_sui.py +0 -261
pgsui/utils/sequence_tools.py +0 -407
simulation/sim_benchmarks.py +0 -333
simulation/sim_treeparams.py +0 -475
test/__init__.py +0 -0
test/pg_sui_simtest.py +0 -215
test/pg_sui_testing.py +0 -523
test/test.py +0 -151
test/test_pgsui.py +0 -374
test/test_tkc.py +0 -185

pgsui/example_data/trees/test_siterates.txt DELETED Viewed

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pg-sui 0.2.3__py3-none-any.whl → 1.6.16a3__py3-none-any.whl

pg-sui 0.2.3py3-none-any.whl → 1.6.16a3py3-none-any.whl