PyPI - pg-sui - Versions diffs - 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl - Mend

pg-sui 1.0.2.1py3-none-any.whl → 1.6.8py3-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.

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{pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/METADATA +51 -70
pg_sui-1.6.8.dist-info/RECORD +78 -0
{pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/WHEEL +1 -1
pg_sui-1.6.8.dist-info/entry_points.txt +4 -0
pg_sui-1.6.8.dist-info/top_level.txt +1 -0
pgsui/__init__.py +35 -54
pgsui/_version.py +34 -0
pgsui/cli.py +635 -0
pgsui/data_processing/config.py +576 -0
pgsui/data_processing/containers.py +1782 -0
pgsui/data_processing/transformers.py +121 -1103
pgsui/electron/app/__main__.py +5 -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 +189 -0
pgsui/electron/app/package-lock.json +6893 -0
pgsui/electron/app/package.json +50 -0
pgsui/electron/app/preload.js +15 -0
pgsui/electron/app/server.py +146 -0
pgsui/electron/app/ui/logo.png +0 -0
pgsui/electron/app/ui/renderer.js +130 -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 +59 -0
pgsui/electron/package.json +14 -0
pgsui/example_data/popmaps/{test.popmap → phylogen_nomx.popmap} +185 -99
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/deterministic/imputers/allele_freq.py +691 -0
pgsui/impute/deterministic/imputers/mode.py +679 -0
pgsui/impute/deterministic/imputers/nmf.py +221 -0
pgsui/impute/deterministic/imputers/phylo.py +971 -0
pgsui/impute/deterministic/imputers/ref_allele.py +530 -0
pgsui/impute/supervised/base.py +339 -0
pgsui/impute/supervised/imputers/hist_gradient_boosting.py +293 -0
pgsui/impute/supervised/imputers/random_forest.py +287 -0
pgsui/impute/unsupervised/base.py +924 -0
pgsui/impute/unsupervised/callbacks.py +89 -263
pgsui/impute/unsupervised/imputers/autoencoder.py +972 -0
pgsui/impute/unsupervised/imputers/nlpca.py +1264 -0
pgsui/impute/unsupervised/imputers/ubp.py +1288 -0
pgsui/impute/unsupervised/imputers/vae.py +957 -0
pgsui/impute/unsupervised/loss_functions.py +158 -0
pgsui/impute/unsupervised/models/autoencoder_model.py +208 -558
pgsui/impute/unsupervised/models/nlpca_model.py +149 -468
pgsui/impute/unsupervised/models/ubp_model.py +198 -1317
pgsui/impute/unsupervised/models/vae_model.py +259 -618
pgsui/impute/unsupervised/nn_scorers.py +215 -0
pgsui/utils/classification_viz.py +591 -0
pgsui/utils/misc.py +35 -480
pgsui/utils/plotting.py +514 -824
pgsui/utils/scorers.py +212 -438
pg_sui-1.0.2.1.dist-info/RECORD +0 -75
pg_sui-1.0.2.1.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 -735
pgsui/impute/impute.py +0 -1486
pgsui/impute/simple_imputers.py +0 -1439
pgsui/impute/supervised/iterative_imputer_fixedparams.py +0 -785
pgsui/impute/supervised/iterative_imputer_gridsearch.py +0 -1027
pgsui/impute/unsupervised/keras_classifiers.py +0 -702
pgsui/impute/unsupervised/models/in_development/cnn_model.py +0 -486
pgsui/impute/unsupervised/neural_network_imputers.py +0 -1424
pgsui/impute/unsupervised/neural_network_methods.py +0 -1549
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 -297
test/test_pgsui.py +0 -374
test/test_tkc.py +0 -214
{pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info/licenses}/LICENSE +0 -0
/pgsui/{example_data/trees → electron/app}/__init__.py +0 -0
/pgsui/impute/{unsupervised/models/in_development → supervised/imputers}/__init__.py +0 -0
{simulation → pgsui/impute/unsupervised/imputers}/__init__.py +0 -0

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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-20	2.78146	2	2.84311
-21	0.46007	1	0.41526
-22	3.10141	2	2.84311
-23	0.65251	1	0.41526
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-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 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl

Potentially problematic release.

pg-sui 1.0.2.1py3-none-any.whl → 1.6.8py3-none-any.whl