Ag3 cohorts analysis version 20250502

A new cohorts analysis version 20250502 has been released for the Ag3 data resource. This is now the default cohorts analysis version when using the malariagen_data Ag3 API. This cohorts analysis will be available for datasets up to and including Ag3.15.

Please note that the new cohorts analysis may change the values of sample metadata columns including taxon, admin1_iso, admin1_name, admin2_name, and derived columns beginning cohorts_ relative to previous cohorts analysis versions.

To pin this cohorts analysis when accessing data:

import malariagen_data

ag3 = malariagen_data.Ag3(
    cohorts_analysis="20250502",
)

This new version introduces some key changes:

• Samples previously labeled as gcx3 in the taxon field have been renamed to pwani:
  • gcx (gambiae complex cryptic taxa) labels serve as placeholders for groups outside our usual taxonomic assignment
  • Following Mwinyi et al. (2024), the gcx1 group has been renamed to Pwani molecular form
  • 65 samples previously assigned as gcx3, are now labeled as pwani.
    • 54 samples from AG1000G-KE
    • 11 samples from AG1000G-TZ
  • Cohort names have been updated, e.g. KE-14_gcx3_2012 is now KE-14_pwan_2012
• 3 previously bissau samples have been reclassified as unassigned.
  • 1 sample from 1188-VO-NIANG-NIEL-SN-2304-VMF00259
  • 2 samples from 1323-VO-GM-NGWA-VMF00242

If you need to access the previous version of the cohorts analysis, you can pin it using the code in here.