Add ancestry estimation panels

Author: lukfor

cloudgene.pgs.yaml

@@ -137,6 +137,12 @@ workflow:
         property: categories
         category: PGSPanel
 
+    - id: ancestry
+      description: Ancestry Estimation
+      type: app_list
+      required: false
+      category: AncestryPanel
+
     - id: myseparator
       type: separator
 

tests/data/input/ancestry/HGDP_238_chr22.RefPC.coord

@@ -0,0 +1,239 @@
+popID	indivID	PC1	PC2	PC3
+Brahui	HGDP00001	3.89674	-23.8954	-1.05304
+Brahui	HGDP00003	0.935253	-18.2278	4.57663
+Brahui	HGDP00011	2.20852	-16.1187	2.63289
+Brahui	HGDP00025	-2.32511	-18.9684	-7.48582
+Brahui	HGDP00027	-9.67688	-8.16514	3.24776
+Balochi	HGDP00057	12.4896	-6.36287	-3.52939
+Balochi	HGDP00074	-4.29351	-14.1138	0.547722
+Balochi	HGDP00082	-1.03311	-19.1594	3.77211
+Balochi	HGDP00086	0.42219	-18.3785	8.16418
+Hazara	HGDP00109	-15.2825	3.043	8.73161
+Hazara	HGDP00119	-5.84947	-9.92489	2.70223
+Hazara	HGDP00120	-14.5381	-2.47754	3.49746
+Hazara	HGDP00122	-9.30642	-8.34555	5.28952
+Hazara	HGDP00125	-18.8599	3.5857	6.01643
+Hazara	HGDP00127	-16.1551	7.47245	-0.0548797
+Makrani	HGDP00131	0.0159989	-15.8076	6.06776
+Makrani	HGDP00133	-2.33469	-14.5696	6.83723
+Sindhi	HGDP00175	27.7593	8.15755	1.87782
+Sindhi	HGDP00183	-4.69389	-8.01844	4.84524
+Sindhi	HGDP00187	-2.89961	-8.94196	3.3437
+Sindhi	HGDP00205	-2.31218	-15.9341	2.40069
+Sindhi	HGDP00210	-2.69748	-17.4291	1.80611
+Pathan	HGDP00214	-3.71892	-10.7085	-1.66817
+Pathan	HGDP00226	-1.99222	-17.8296	-6.33738
+Pathan	HGDP00234	-5.02875	-15.2521	-1.15767
+Kalash	HGDP00274	-4.50277	-15.4928	-0.576923
+Kalash	HGDP00279	-1.15825	-12.5538	5.42106
+Kalash	HGDP00285	-2.33269	-21.3511	4.18123
+Kalash	HGDP00290	-5.58448	-15.7249	-6.83048
+Kalash	HGDP00298	-4.78716	-19.6104	-2.09788
+Kalash	HGDP00304	-5.92313	-13.0848	0.000966304
+Kalash	HGDP00315	-4.81528	-9.97073	0.161677
+Kalash	HGDP00330	1.61258	-18.6116	-0.163756
+Burusho	HGDP00336	-0.620166	-19.413	3.21236
+Burusho	HGDP00359	-3.71493	-14.6913	3.48772
+Burusho	HGDP00371	-6.47435	-10.8311	2.16799
+Burusho	HGDP00372	-4.31866	-17.321	-3.71248
+Burusho	HGDP00397	-2.23816	-14.3504	1.51166
+Burusho	HGDP00402	-7.11215	-10.6041	0.321564
+Burusho	HGDP00407	-4.69858	-9.44484	-1.24942
+Burusho	HGDP00433	-6.59963	-5.98897	-0.0490039
+Burusho	HGDP00445	-2.74726	-15.9895	-0.988051
+MbutiPygmy	HGDP00450	68.9482	34.4484	-3.86755
+BiakaPygmy	HGDP00454	74.0183	35.5486	-4.80803
+BiakaPygmy	HGDP00465	68.5033	32.2953	-0.512854
+MbutiPygmy	HGDP00467	63.4522	31.5823	-4.64809
+BiakaPygmy	HGDP00470	70.8496	34.9222	-3.86677
+BiakaPygmy	HGDP00472	72.2884	36.4221	-4.70435
+MbutiPygmy	HGDP00474	67.0025	31.276	-8.20961
+Melanesian	HGDP00491	-17.7768	20.6534	31.8449
+French	HGDP00511	0.865585	-29.4425	-1.46347
+French	HGDP00520	0.857896	-23.8532	-0.435498
+French	HGDP00530	1.5799	-30.7966	-1.80844
+French	HGDP00534	1.67787	-24.9134	-7.12049
+Papuan	HGDP00541	-18.619	20.6901	34.4792
+Papuan	HGDP00542	-18.5791	21.4466	34.8013
+Papuan	HGDP00547	-17.3005	19.5276	33.9092
+Papuan	HGDP00555	-14.3738	21.2872	24.7514
+Druze	HGDP00580	6.57082	-24.6351	1.77299
+Druze	HGDP00595	4.2847	-25.6268	-3.8062
+Druze	HGDP00597	4.81188	-29.7219	0.504068
+Druze	HGDP00600	2.76448	-26.3603	1.92108
+Druze	HGDP00601	8.05274	-22.0387	1.71179
+Druze	HGDP00602	5.95359	-16.0046	-0.90125
+Druze	HGDP00606	3.5309	-27.2452	-0.205312
+Bedouin	HGDP00607	10.1952	-17.4682	-0.0929838
+Bedouin	HGDP00609	3.40292	-15.6701	1.6001
+Bedouin	HGDP00610	4.31487	-26.441	2.99283
+Bedouin	HGDP00611	18.7836	-6.98035	-1.20798
+Bedouin	HGDP00613	2.11497	-27.5929	4.80809
+Bedouin	HGDP00616	11.6228	-23.9071	1.6054
+Bedouin	HGDP00618	7.55959	-22.4814	0.805438
+Bedouin	HGDP00619	2.76219	-26.3232	4.11036
+Bedouin	HGDP00629	11.4232	-18.6657	-0.874795
+Bedouin	HGDP00630	13.468	-26.2498	-1.09227
+Bedouin	HGDP00636	12.5478	-22.6438	5.67612
+Bedouin	HGDP00645	2.91482	-16.9984	4.34442
+Bedouin	HGDP00649	9.19164	-23.6541	-3.67058
+Bedouin	HGDP00650	13.2578	-24.3093	-3.44946
+Bedouin	HGDP00653	4.65336	-28.4848	-0.172708
+Melanesian	HGDP00655	-17.116	21.3264	29.7417
+Melanesian	HGDP00979	-18.7581	20.6035	35.1989
+Melanesian	HGDP00663	-14.8525	19.0107	32.2157
+Melanesian	HGDP00664	-17.6193	20.078	31.7127
+Sardinian	HGDP00666	4.0079	-25.5005	1.95532
+Sardinian	HGDP00672	4.20076	-31.0075	6.32575
+Sardinian	HGDP00673	2.7213	-30.4829	-1.27987
+Palestinian	HGDP00677	13.0249	-21.9362	3.29666
+Palestinian	HGDP00678	9.18138	-28.1511	3.17038
+Palestinian	HGDP00679	8.44716	-23.574	0.284705
+Palestinian	HGDP00680	9.84227	-21.365	4.46118
+Palestinian	HGDP00682	5.50487	-19.5395	2.19111
+Palestinian	HGDP00686	8.93169	-19.4876	-0.45776
+Palestinian	HGDP00688	11.1334	-25.0896	5.10378
+Palestinian	HGDP00696	-0.621434	-19.4185	-7.86581
+Palestinian	HGDP00699	12.3672	-18.3367	-0.340808
+Bedouin	HGDP00701	11.6389	-19.9099	2.86147
+Colombian	HGDP00706	-31.4653	18.0451	-50.5118
+Colombian	HGDP00708	-25.4639	19.5998	-53.8412
+Colombian	HGDP00710	-28.0676	16.9843	-55.042
+Cambodian	HGDP00713	-24.0026	20.0078	9.17214
+Cambodian	HGDP00720	-20.5068	21.0711	17.6876
+Palestinian	HGDP00722	3.09345	-18.9814	3.333
+Palestinian	HGDP00727	8.9466	-26.02	6.37837
+Palestinian	HGDP00730	14.1872	-19.8363	3.96956
+Palestinian	HGDP00732	4.95233	-18.9546	-0.728737
+Palestinian	HGDP00733	10.3074	-22.8131	-5.75545
+Palestinian	HGDP00737	11.5607	-19.9843	0.0758168
+Palestinian	HGDP00738	8.43544	-21.8759	4.50267
+Palestinian	HGDP00739	10.2976	-26.3666	3.53329
+Palestinian	HGDP00740	3.01728	-18.9988	0.4637
+Palestinian	HGDP00744	10.4807	-27.6739	-1.90033
+Palestinian	HGDP00745	4.95777	-23.0577	-6.24862
+Han	HGDP00774	-24.7552	26.2584	13.883
+Han	HGDP00776	-22.2959	29.8395	10.624
+Han	HGDP00777	-29.4391	25.2174	13.0288
+Han	HGDP00778	-29.635	24.1723	9.49016
+Han	HGDP00779	-28.5146	26.6393	14.5724
+Han	HGDP00781	-25.3812	32.0567	14.3165
+Han	HGDP00786	-30.2144	29.4008	14.3215
+Orcadian	HGDP00806	-3.40207	-27.7022	0.400497
+Han	HGDP00813	-27.0995	23.8665	15.4338
+Han	HGDP00814	-27.6271	26.8179	15.9232
+Surui	HGDP00838	-28.3929	16.2469	-63.345
+Surui	HGDP00843	-27.2838	16.185	-58.9008
+Surui	HGDP00845	-28.3405	21.0549	-55.292
+Maya	HGDP00857	-25.8413	16.3828	-41.4344
+Maya	HGDP00861	-4.73792	18.6095	-35.2721
+Maya	HGDP00872	-27.0498	19.9682	-48.32
+Maya	HGDP00875	-28.5014	15.0049	-47.4756
+Maya	HGDP00876	-23.8302	8.4391	-35.5192
+Maya	HGDP00877	-26.3055	13.4058	-41.3746
+Russian	HGDP00879	-1.85085	-18.851	2.86299
+Russian	HGDP00880	1.03218	-25.4223	3.11962
+Russian	HGDP00882	-4.72327	-10.7047	-0.876024
+Russian	HGDP00884	-0.654118	-24.8596	-3.61283
+Russian	HGDP00889	1.07762	-25.3927	-1.22481
+Russian	HGDP00893	-1.1083	-15.7477	3.54781
+Russian	HGDP00895	-3.97251	-21.7099	-6.39567
+Russian	HGDP00897	-5.18748	-18.7242	1.92514
+Russian	HGDP00902	-5.6646	-16.2845	-4.35744
+Mandenka	HGDP00909	66.3122	27.727	0.694621
+Mandenka	HGDP00911	64.2059	26.9734	-3.07705
+Mandenka	HGDP00915	64.0312	26.0119	0.169609
+Yoruba	HGDP00925	67.118	31.4531	-1.48784
+Yoruba	HGDP00926	65.1075	25.5294	0.9728
+Yoruba	HGDP00929	67.4486	31.9388	-6.27727
+Yoruba	HGDP00935	61.0972	30.2185	-4.19691
+Yoruba	HGDP00942	65.8168	26.8075	-4.38249
+Yakut	HGDP00945	-28.4599	28.5813	6.00269
+Yakut	HGDP00954	-24.5683	22.6085	3.49126
+Yakut	HGDP00956	-29.7529	21.0096	7.96416
+Yakut	HGDP00959	-27.6664	24.2492	-0.229017
+Yakut	HGDP00962	-21.3628	22.4931	7.1398
+Yakut	HGDP00964	-20.1435	10.376	10.8736
+Colombian	HGDP00970	-26.1675	11.9499	-60.5805
+BiakaPygmy	HGDP00985	71.2147	35.7913	-1.19813
+San	HGDP00992	63.0453	33.2549	-4.41696
+Karitiana	HGDP01003	-29.4689	17.0973	-54.6494
+Karitiana	HGDP01010	-30.3064	17.7283	-44.3363
+Karitiana	HGDP01013	-29.2648	16.6279	-53.8299
+Melanesian	HGDP01027	-17.9013	21.5106	27.1244
+San	HGDP01029	68.0364	34.4366	-4.83388
+BantuSouthAfrica	HGDP01031	69.3433	33.6941	-2.73157
+Pima	HGDP01037	-26.5196	19.1949	-43.0202
+Pima	HGDP01051	-23.8799	19.3932	-44.1497
+Pima	HGDP01060	-26.3479	15.162	-46.8449
+Sardinian	HGDP01063	3.06206	-27.9991	1.56461
+Sardinian	HGDP01078	3.27027	-29.7428	5.07858
+MbutiPygmy	HGDP01081	71.7769	32.4077	-5.0661
+Tujia	HGDP01096	-22.9971	25.132	13.8485
+Tujia	HGDP01097	-26.8352	25.8107	14.2767
+Tujia	HGDP01103	-27.5491	26.696	17.4364
+Tujia	HGDP01104	-24.3064	28.1075	13.4351
+Italian	HGDP01153	-1.42451	-22.0091	4.08139
+Tuscan	HGDP01164	4.97147	-31.8575	-3.22347
+Italian	HGDP01172	2.3236	-26.6485	2.01467
+Italian	HGDP01174	8.48022	-26.0764	6.26373
+Italian	HGDP01177	5.22177	-30.4644	0.8951
+Yi	HGDP01180	-25.1658	24.4315	14.7034
+Yi	HGDP01182	-25.0215	24.9957	14.3363
+Yi	HGDP01184	-19.626	19.7562	14.2479
+Oroqen	HGDP01207	-21.4002	22.6318	-0.732056
+Daur	HGDP01213	-28.9482	29.7332	8.6938
+Daur	HGDP01216	-26.7347	22.0751	9.27732
+Mongola	HGDP01223	-22.9147	17.4613	6.72201
+Mongola	HGDP01226	-21.6406	14.5322	6.68716
+Mongola	HGDP01227	-24.7718	26.2414	7.99433
+Mongola	HGDP01228	-22.9116	20.706	4.31543
+Hezhen	HGDP01237	-25.2119	23.3819	10.4071
+Hezhen	HGDP01240	-28.1852	24.0066	9.48833
+Hezhen	HGDP01241	-28.8366	29.1992	6.35387
+Hezhen	HGDP01242	-25.3547	30.4461	8.95491
+Xibo	HGDP01247	-23.0553	19.3062	3.43851
+Mozabite	HGDP01255	11.943	-17.9003	2.61179
+Mozabite	HGDP01269	9.22592	-24.3837	1.41492
+Mozabite	HGDP01272	14.4796	-18.3362	-0.141572
+Mozabite	HGDP01273	19.5313	-22.1466	6.64176
+Mandenka	HGDP01283	63.7705	19.4979	-1.18599
+Mandenka	HGDP01285	63.0503	27.0898	-0.990653
+Mandenka	HGDP01286	60.3858	27.6195	-1.41018
+Han-NChina	HGDP01287	-24.6766	26.4134	10.2509
+Han-NChina	HGDP01290	-26.7386	17.219	13.2053
+Uygur	HGDP01302	-15.3246	4.13857	2.43682
+Dai	HGDP01312	-27.6536	27.6312	8.59732
+Lahu	HGDP01318	-24.6763	24.2951	13.7089
+Lahu	HGDP01321	-23.4337	27.8147	14.4282
+Lahu	HGDP01322	-23.4455	27.3342	9.97125
+Lahu	HGDP01323	-24.937	27.0094	14.6343
+She	HGDP01332	-26.1016	21.6748	14.1902
+Naxi	HGDP01337	-26.913	24.4396	9.76037
+Naxi	HGDP01339	-25.8063	29.093	12.9176
+Tu	HGDP01347	-24.5606	23.6505	15.1719
+Tu	HGDP01348	-21.2914	20.785	7.90193
+Tu	HGDP01349	-21.4932	15.0862	5.77261
+Tu	HGDP01356	-23.04	15.7606	11.7881
+Basque	HGDP01358	2.07128	-28.0501	-0.570791
+Basque	HGDP01361	-0.202892	-24.6844	2.8193
+Basque	HGDP01362	2.30368	-30.612	-4.93169
+Basque	HGDP01363	-3.54107	-26.9922	0.889519
+Basque	HGDP01366	0.797603	-33.3527	2.77206
+Basque	HGDP01367	2.94772	-27.6645	3.59631
+Basque	HGDP01368	-3.4515	-25.5498	0.656437
+Basque	HGDP01371	3.53554	-26.5866	3.38597
+Basque	HGDP01373	0.0176421	-31.6638	-1.90245
+Basque	HGDP01380	-0.525172	-23.945	0.681262
+Adygei	HGDP01384	1.26669	-24.8193	1.67644
+Adygei	HGDP01388	-2.00207	-23.7514	4.50852
+Adygei	HGDP01402	3.95393	-23.9437	-2.81254
+Adygei	HGDP01403	1.63326	-27.4392	-0.231083
+BantuKenya	HGDP01405	66.3059	26.3745	-2.11563
+BantuKenya	HGDP01418	67.7846	29.4991	-5.19068
+BantuKenya	HGDP01419	60.6245	24.9429	-0.781842
+Han	HGDP01024	-26.93	23.7946	8.46314
+Cambodian	HGDP00719	-23.7944	24.9895	16.1259
+French	HGDP00516	1.85225	-28.7163	0.441455
+Tu	HGDP01354	-27.4193	23.9007	10.7239
+Sardinian	HGDP01070	3.93802	-26.3136	2.13519

tests/data/input/ancestry/HGDP_238_chr22.RefPC.var

@@ -0,0 +1,9 @@
+PC	Variance(%)
+1	6.86641
+2	4.9517
+3	2.60941
+4	1.6994
+5	1.0154
+6	0.964353
+7	0.875485
+8	0.829739