The Biogeographical groups are inside study_parameters. These are now added to the var_pheno_ann and var_drug_ann files (deduplicated if more than study was done per annotation)
There is an extra file with manually curated biogroup - association id that potentially deconvolutes the biogroups in the 7 defined by pharmgkb. If we use it, manual curation should be revised (see functions to incorporate that in study_parameters.py)
The Biogeographical groups are inside study_parameters. These are now added to the
var_pheno_ann
andvar_drug_ann
files (deduplicated if more than study was done per annotation) There is an extra file with manually curated biogroup - association id that potentially deconvolutes the biogroups in the 7 defined by pharmgkb. If we use it, manual curation should be revised (see functions to incorporate that instudy_parameters.py
)