File size: 1,310 Bytes
0161e74 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 |
MAJOR_TISSUE_LIST = ["heart", "blood", "brain", "lung", "kidney", "intestine", "pancreas"]
VERSION = "2023-05-08"
CANCER_LIST_PATH = "./cancer_list.txt"
with open(CANCER_LIST_PATH) as f:
CANCER_LIST = [line.rstrip('\n') for line in f]
# build the value filter dict for each tissue
VALUE_FILTER = {
tissue : f"suspension_type != 'na' and disease == 'normal' and tissue_general == '{tissue}'" for tissue in MAJOR_TISSUE_LIST
}
# build the value filter dict for cells related with other tissues
# since tileDB does not support `not in ` operator, we will just use `!=` to filter out the other tissues
VALUE_FILTER["others"] = f"suspension_type != 'na' and disease == 'normal'"
for tissue in MAJOR_TISSUE_LIST:
VALUE_FILTER["others"] = f"{VALUE_FILTER['others']} and (tissue_general != '{tissue}')"
VALUE_FILTER['pan-cancer'] = f"suspension_type != 'na'"
cancer_condition = ""
for disease in CANCER_LIST:
if cancer_condition == "":
cancer_condition = f"(disease == '{disease}')"
else:
cancer_condition = f"{cancer_condition} or (disease == '{disease}')"
VALUE_FILTER['pan-cancer'] = f"(suspension_type != 'na') and ({cancer_condition})"
if __name__ == "__main__":
# print(VALUE_FILTER["others"])
# print(MAJOR_TISSUE_LIST)
print(VALUE_FILTER['pan-cancer'])
|