Access cohort metadata through the malariagen_data Python API

A new function has been added to the the malariagen_data Python API allowing users to access cohort sample metadata including cohort size, country code, taxon, administrative units name, ISO code, geoBoundaries shape ID and representative latitude and longitude points. Below are some examples for data from the Anopheles gambiae complex accessed via the Ag3 API.

import malariagen_data
ag3 = malariagen_data.Ag3()

The cohort sets that can be accessed include "admin1_month", "admin1_quarter", "admin1_year", "admin2_month", "admin2_quarter", "admin2_year". Below are the cohort sets for "admin1_month".

ag3.cohorts('admin1_month')

	cohort_id	cohort_size	country	country_alpha2	country_alpha3	taxon	year	quarter	month	admin1_name	admin1_iso	admin1_geoboundaries_shape_id	admin1_representative_longitude	admin1_representative_latitude
0	AO-LUA_colu_2009_04	81	Angola	AO	AGO	coluzzii	2009	2	4	Luanda	AO-LUA	26408823B49174064004395	13.679075	-9.592222
1	AO-LUA_colu_2010	8	Angola	AO	AGO	coluzzii	2010	-1	-1	Luanda	AO-LUA	26408823B49174064004395	13.679075	-9.592222
2	BF-01_arab_2008_11	1	Burkina Faso	BF	BFA	arabiensis	2008	4	11	Boucle du Mouhoun	BF-01	92566538B98190668782446	-3.592255	12.479899
3	BF-01_arab_2022_09	6	Burkina Faso	BF	BFA	arabiensis	2022	3	9	Boucle du Mouhoun	BF-01	92566538B98190668782446	-3.592255	12.479899
4	BF-01_arab_2022_11	7	Burkina Faso	BF	BFA	arabiensis	2022	4	11	Boucle du Mouhoun	BF-01	92566538B98190668782446	-3.592255	12.479899
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
710	ZM-08_gamb_2020_09	20	Zambia	ZM	ZMB	gambiae	2020	3	9	Copperbelt	ZM-08	6923714B61812757118010	27.956171	-13.078825
711	ZM-08_gamb_2020_10	46	Zambia	ZM	ZMB	gambiae	2020	4	10	Copperbelt	ZM-08	6923714B61812757118010	27.956171	-13.078825
712	ZM-08_gamb_2020_11	30	Zambia	ZM	ZMB	gambiae	2020	4	11	Copperbelt	ZM-08	6923714B61812757118010	27.956171	-13.078825
713	ZM-08_gamb_2021_03	20	Zambia	ZM	ZMB	gambiae	2021	1	3	Copperbelt	ZM-08	6923714B61812757118010	27.956171	-13.078825
714	ZW18_quad_1986	10	Zimbabwe	ZW	ZWE	quadriannulatus	1986	-1	-1	Masvingo	ZW18	88200057B65333360538194	31.341978	-20.784921

715 rows × 14 columns

As with the sample metadata function, the resulting cohort table can be filtered to individual requirements. For example, below the table is filtered to show cohorts of An. gambiae from Burkina Faso with at least ten individuals.

df_cohorts = ag3.cohorts('admin1_year')

df_cohorts.query('country == "Burkina Faso" and taxon == "gambiae" and cohort_size > 10')

	cohort_id	cohort_size	country	country_alpha2	country_alpha3	taxon	year	admin1_name	admin1_iso	admin1_geoboundaries_shape_id	admin1_representative_longitude	admin1_representative_latitude
13	BF-02_gamb_2022	31	Burkina Faso	BF	BFA	gambiae	2022	Cascades	BF-02	92566538B44525923588019	-4.482810	10.308460
19	BF-07_gamb_2004	13	Burkina Faso	BF	BFA	gambiae	2004	Centre-Sud	BF-07	92566538B93881058138595	-1.054201	11.581508
20	BF-07_gamb_2022	18	Burkina Faso	BF	BFA	gambiae	2022	Centre-Sud	BF-07	92566538B93881058138595	-1.054201	11.581508
23	BF-08_gamb_2022	40	Burkina Faso	BF	BFA	gambiae	2022	Est	BF-08	92566538B65349096386527	1.011924	12.254145
42	BF-09_gamb_2012	103	Burkina Faso	BF	BFA	gambiae	2012	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
43	BF-09_gamb_2014	168	Burkina Faso	BF	BFA	gambiae	2014	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
44	BF-09_gamb_2015	141	Burkina Faso	BF	BFA	gambiae	2015	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
45	BF-09_gamb_2016	104	Burkina Faso	BF	BFA	gambiae	2016	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
46	BF-09_gamb_2017	52	Burkina Faso	BF	BFA	gambiae	2017	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
47	BF-09_gamb_2018	18	Burkina Faso	BF	BFA	gambiae	2018	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
48	BF-09_gamb_2019	16	Burkina Faso	BF	BFA	gambiae	2019	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423
51	BF-09_gamb_2022	20	Burkina Faso	BF	BFA	gambiae	2022	Hauts-Bassins	BF-09	92566538B40583601847470	-4.032051	11.387423

The cohorts function is also avaliable for use with the Anopheles funestus data release Af1(). For questions on usage please send a request to support@malariagen.net.