paths.toml

### paths to downstream dsets:
APTOS_PATH = "/PATH/TO/APTOS/"
PALM_PATH = "/PATH/TO/PALM/PALM-Training400/"
RFMID_PATH = "/PATH/TO/RFMiD/"

### model paths

CHECKPOINTS_BASE_PATH = "checkpoints/"


### software

# should point to the executables
PLINK1 = "/PATH/TO/plink/plink"
PLINK2 = "/PATH/TO/plink2/plink2"

### UKB paths

# phenotype file provided as is from UKB
UKB_PHENO_FILE = "/PATH/TO/ukbXXXXXX_full.csv"
# can be kept as is - will be created automatically
PATH_TO_COV = 'data/covariates_card.csv'

# BASE_IMG + {LEFT|RIGHT}_SUBDIR should contain all available fundus images after preprocessing
BASE_IMG = "/PATH/TO/retinal_fundus/"
LEFT_SUBDIR = "left/512_left/processed/"
RIGHT_SUBDIR = "right/512_right/processed/"

# path to bed files. directory should contain the `ukb_chr{1..22}_v2.{bed|fam|bim} files
BASE_GEN = "/PATH/TO/microarray/"

ANCESTRY = "/PATH/TO/UKBB.w_hm3.AllAncestry.model_pred"
BASE_PGS = "/PATH/TO/precomputed_pgs/"

# directory for preprocessed burden data
# contains the files: combined_burdens_colnames.txt, combined_burdens_iid.txt, combined_burdens.h5
BASE_BURDEN = "PATH/TO/burdens/"

# ignore this! Processed biomarkers; not used in the experiments
BLOOD_BIOMARKERS = ""