PyPI - pg-sui - Versions diffs - 0.2.0__py3-none-any.whl → 1.6.14.dev9__py3-none-any.whl - Mend

pg-sui 0.2.0py3-none-any.whl → 1.6.14.dev9py3-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 (127) hide show

{pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info}/METADATA +101 -79
pg_sui-1.6.14.dev9.dist-info/RECORD +81 -0
{pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info}/WHEEL +1 -1
pg_sui-1.6.14.dev9.dist-info/entry_points.txt +4 -0
{pg_sui-0.2.0.dist-info → pg_sui-1.6.14.dev9.dist-info/licenses}/LICENSE +0 -0
pg_sui-1.6.14.dev9.dist-info/top_level.txt +1 -0
pgsui/__init__.py +35 -54
pgsui/_version.py +34 -0
pgsui/cli.py +909 -0
pgsui/data_processing/__init__.py +0 -0
pgsui/data_processing/config.py +565 -0
pgsui/data_processing/containers.py +1424 -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 +1118 -0
pgsui/impute/unsupervised/callbacks.py +92 -262
{simulation → pgsui/impute/unsupervised/imputers}/__init__.py +0 -0
pgsui/impute/unsupervised/imputers/autoencoder.py +1285 -0
pgsui/impute/unsupervised/imputers/nlpca.py +1554 -0
pgsui/impute/unsupervised/imputers/ubp.py +1575 -0
pgsui/impute/unsupervised/imputers/vae.py +1228 -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-0.2.0.dist-info/RECORD +0 -75
pg_sui-0.2.0.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.rate DELETED Viewed

@@ -1,2033 +0,0 @@
-# Site-specific subtitution rates determined by empirical Bayesian method
-# This file can be read in MS Excel or in R with command:
-#   tab=read.table('test.phy.rate',header=TRUE)
-# Columns are tab-separated with following meaning:
-#   Site:   Alignment site ID
-#   Rate:   Posterior mean site rate weighted by posterior probability
-#   Cat:    Category with highest posterior (0=invariable, 1=slow, etc)
-#   C_Rate: Corresponding rate of highest category
-Site	Rate	Cat	C_Rate
-1	0.65244	1	0.41526
-2	0.71905	1	0.41526
-3	0.66729	1	0.41526
-4	2.65438	2	2.84311
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-18	0.45609	1	0.41526
-19	0.46272	1	0.41526
-20	2.78146	2	2.84311
-21	0.46007	1	0.41526
-22	3.10141	2	2.84311
-23	0.65251	1	0.41526
-24	0.41980	1	0.41526
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-32	0.45676	1	0.41526
-33	0.42065	1	0.41526
-34	11.38813	3	11.47065
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-1784	0.45586	1	0.41526
-1785	0.46380	1	0.41526
-1786	0.46253	1	0.41526
-1787	0.45533	1	0.41526
-1788	0.45261	1	0.41526
-1789	0.69839	1	0.41526
-1790	0.65968	1	0.41526
-1791	0.67098	1	0.41526
-1792	0.70394	1	0.41526
-1793	1.86677	2	2.84311
-1794	0.45266	1	0.41526
-1795	0.70517	1	0.41526
-1796	0.70314	1	0.41526
-1797	0.46114	1	0.41526
-1798	10.63547	3	11.47065
-1799	0.45553	1	0.41526
-1800	0.60370	1	0.41526
-1801	0.46316	1	0.41526
-1802	0.69493	1	0.41526
-1803	0.42002	1	0.41526
-1804	0.46811	1	0.41526
-1805	0.45454	1	0.41526
-1806	0.66675	1	0.41526
-1807	0.44214	1	0.41526
-1808	0.65298	1	0.41526
-1809	0.42101	1	0.41526
-1810	0.45694	1	0.41526
-1811	3.91135	2	2.84311
-1812	0.41943	1	0.41526
-1813	0.60020	1	0.41526
-1814	0.45359	1	0.41526
-1815	0.45235	1	0.41526
-1816	0.44903	1	0.41526
-1817	0.45187	1	0.41526
-1818	0.41984	1	0.41526
-1819	0.45323	1	0.41526
-1820	0.42038	1	0.41526
-1821	0.46066	1	0.41526
-1822	0.58941	1	0.41526
-1823	0.66404	1	0.41526
-1824	0.45207	1	0.41526
-1825	0.45042	1	0.41526
-1826	3.50787	2	2.84311
-1827	0.41905	1	0.41526
-1828	0.73727	1	0.41526
-1829	0.71406	1	0.41526
-1830	0.43930	1	0.41526
-1831	0.45193	1	0.41526
-1832	0.45342	1	0.41526
-1833	0.67909	1	0.41526
-1834	0.46209	1	0.41526
-1835	0.41898	1	0.41526
-1836	0.45329	1	0.41526
-1837	0.47054	1	0.41526
-1838	0.44856	1	0.41526
-1839	0.42010	1	0.41526
-1840	0.66348	1	0.41526
-1841	0.45610	1	0.41526
-1842	1.47401	1	0.41526
-1843	0.41902	1	0.41526
-1844	0.46069	1	0.41526
-1845	0.41879	1	0.41526
-1846	0.46617	1	0.41526
-1847	0.45629	1	0.41526
-1848	1.55109	1	0.41526
-1849	0.41945	1	0.41526
-1850	0.45855	1	0.41526
-1851	0.45449	1	0.41526
-1852	0.45562	1	0.41526
-1853	0.69011	1	0.41526
-1854	0.69390	1	0.41526
-1855	1.73267	2	2.84311
-1856	0.45660	1	0.41526
-1857	0.46719	1	0.41526
-1858	0.46684	1	0.41526
-1859	0.46375	1	0.41526
-1860	0.45467	1	0.41526
-1861	0.44045	1	0.41526
-1862	0.44887	1	0.41526
-1863	0.45230	1	0.41526
-1864	0.46139	1	0.41526
-1865	0.41950	1	0.41526
-1866	0.45931	1	0.41526
-1867	0.43938	1	0.41526
-1868	0.41847	1	0.41526
-1869	0.43804	1	0.41526
-1870	11.45728	3	11.47065
-1871	0.41904	1	0.41526
-1872	0.69073	1	0.41526
-1873	0.45623	1	0.41526
-1874	0.43952	1	0.41526
-1875	0.41911	1	0.41526
-1876	0.61178	1	0.41526
-1877	0.64555	1	0.41526
-1878	0.45228	1	0.41526
-1879	0.57677	1	0.41526
-1880	0.46566	1	0.41526
-1881	0.46219	1	0.41526
-1882	0.45372	1	0.41526
-1883	0.46070	1	0.41526
-1884	0.45467	1	0.41526
-1885	0.44015	1	0.41526
-1886	0.46142	1	0.41526
-1887	0.45784	1	0.41526
-1888	0.41989	1	0.41526
-1889	0.45218	1	0.41526
-1890	0.42063	1	0.41526
-1891	0.45196	1	0.41526
-1892	2.78848	2	2.84311
-1893	0.46027	1	0.41526
-1894	0.46181	1	0.41526
-1895	0.45298	1	0.41526
-1896	0.46408	1	0.41526
-1897	0.46345	1	0.41526
-1898	0.67935	1	0.41526
-1899	2.51303	2	2.84311
-1900	0.66607	1	0.41526
-1901	0.41860	1	0.41526
-1902	4.79796	2	2.84311
-1903	0.46586	1	0.41526
-1904	0.45806	1	0.41526
-1905	0.64805	1	0.41526
-1906	1.68866	2	2.84311
-1907	0.59708	1	0.41526
-1908	2.80209	2	2.84311
-1909	0.45191	1	0.41526
-1910	0.46178	1	0.41526
-1911	0.73925	1	0.41526
-1912	0.68458	1	0.41526
-1913	1.75977	2	2.84311
-1914	0.65366	1	0.41526
-1915	0.67345	1	0.41526
-1916	0.45905	1	0.41526
-1917	0.46024	1	0.41526
-1918	0.41980	1	0.41526
-1919	0.42070	1	0.41526
-1920	0.41858	1	0.41526
-1921	0.41884	1	0.41526
-1922	0.45976	1	0.41526
-1923	0.42148	1	0.41526
-1924	0.41873	1	0.41526
-1925	0.44526	1	0.41526
-1926	0.46906	1	0.41526
-1927	0.72561	1	0.41526
-1928	0.66629	1	0.41526
-1929	0.45224	1	0.41526
-1930	0.41998	1	0.41526
-1931	0.46647	1	0.41526
-1932	5.15888	2	2.84311
-1933	0.45571	1	0.41526
-1934	2.55503	2	2.84311
-1935	0.68775	1	0.41526
-1936	0.58841	1	0.41526
-1937	0.44364	1	0.41526
-1938	1.59556	1	0.41526
-1939	4.54932	2	2.84311
-1940	0.45912	1	0.41526
-1941	0.41922	1	0.41526
-1942	0.45513	1	0.41526
-1943	11.42852	3	11.47065
-1944	0.41847	1	0.41526
-1945	0.46617	1	0.41526
-1946	0.66169	1	0.41526
-1947	0.45932	1	0.41526
-1948	0.45869	1	0.41526
-1949	0.46359	1	0.41526
-1950	0.42007	1	0.41526
-1951	0.45616	1	0.41526
-1952	0.69493	1	0.41526
-1953	0.71794	1	0.41526
-1954	0.68327	1	0.41526
-1955	0.45984	1	0.41526
-1956	0.69576	1	0.41526
-1957	0.66369	1	0.41526
-1958	0.64549	1	0.41526
-1959	0.44466	1	0.41526
-1960	0.45505	1	0.41526
-1961	1.61419	1	0.41526
-1962	0.45258	1	0.41526
-1963	0.46368	1	0.41526
-1964	0.67936	1	0.41526
-1965	0.42190	1	0.41526
-1966	0.68179	1	0.41526
-1967	0.45219	1	0.41526
-1968	0.41875	1	0.41526
-1969	0.44511	1	0.41526
-1970	11.13529	3	11.47065
-1971	0.46024	1	0.41526
-1972	0.69792	1	0.41526
-1973	0.45341	1	0.41526
-1974	0.41982	1	0.41526
-1975	0.67394	1	0.41526
-1976	1.27897	1	0.41526
-1977	0.69811	1	0.41526
-1978	0.46809	1	0.41526
-1979	0.65168	1	0.41526
-1980	11.41591	3	11.47065
-1981	0.46276	1	0.41526
-1982	0.65155	1	0.41526
-1983	1.60939	1	0.41526
-1984	0.72503	1	0.41526
-1985	1.49277	1	0.41526
-1986	1.77021	2	2.84311
-1987	0.42035	1	0.41526
-1988	0.45225	1	0.41526
-1989	0.45370	1	0.41526
-1990	0.57858	1	0.41526
-1991	4.06903	2	2.84311
-1992	0.46033	1	0.41526
-1993	0.71805	1	0.41526
-1994	0.45570	1	0.41526
-1995	0.44873	1	0.41526
-1996	0.45293	1	0.41526
-1997	11.35720	3	11.47065
-1998	0.44663	1	0.41526
-1999	0.45351	1	0.41526
-2000	0.42032	1	0.41526
-2001	0.46214	1	0.41526
-2002	2.76490	2	2.84311
-2003	0.42019	1	0.41526
-2004	0.65961	1	0.41526
-2005	0.45383	1	0.41526
-2006	0.45949	1	0.41526
-2007	0.45373	1	0.41526
-2008	0.65842	1	0.41526
-2009	0.41895	1	0.41526
-2010	0.46511	1	0.41526
-2011	0.41877	1	0.41526
-2012	11.46205	3	11.47065
-2013	0.41910	1	0.41526
-2014	0.69536	1	0.41526
-2015	0.67322	1	0.41526
-2016	0.45277	1	0.41526
-2017	0.59844	1	0.41526
-2018	0.45635	1	0.41526
-2019	0.45258	1	0.41526
-2020	0.44346	1	0.41526
-2021	0.46447	1	0.41526
-2022	0.41871	1	0.41526
-2023	0.45858	1	0.41526
-2024	0.46142	1	0.41526

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

pg-sui 0.2.0py3-none-any.whl → 1.6.14.dev9py3-none-any.whl