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Correcting update_reference_genome_path pointing it to constants.py #152

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Correcting update_reference_genome_path pointing it to constants.py #152

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5 changes: 1 addition & 4 deletions maxatac/utilities/system_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import sys
import subprocess
from os import path, getcwd, makedirs, error, walk, environ
from maxatac.utilities.constants import CPP_LOG_LEVEL
from maxatac.utilities.constants import CPP_LOG_LEVEL, maxatac_data_path
from re import match
from multiprocessing import cpu_count

Expand Down Expand Up @@ -205,9 +205,6 @@ def update_reference_genome_paths(args):
"""
logging.info(f"Generating Paths for genome build: {args.genome} \n")

# build maxatac data path
maxatac_data_path = os.path.join(os.path.expanduser('~'), "opt", "maxatac", "data")

# build genome specific paths
blacklist_path = os.path.join(maxatac_data_path,
f"{args.genome}/{args.genome}_maxatac_blacklist.bed") # maxATAC extended blacklist as bed
Expand Down