def make_salmon_index(args):
print("salmon ref index is not detected, now creating...")
os.makedirs("/local_volume/tmp_fa/", exist_ok=True)
subprocess.run([
"wget", "--quite", "--quota=0", "-O",
"/local_volume/tmp_fa/salmon_ref.fa.gz", args.salmon_ref_dl
])
subprocess.run(["gunzip", "/local_volume/tmp_fa/salmon_ref.fa.gz"])
salmon_index_cmd = Command("salmon index")
salmon_index_cmd_params = {
"-t": "/local_volume/tmp_fa/salmon_ref.fa",
"-i": "/local_volume/salmon_ref_index"
}
salmon_index_cmd.parse_params_dict(salmon_index_cmd_params)
salmon_index_cmd.run()
shutil.rmtree("/local_volume/tmp_fa")
from function import Command, update_params
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--fastqc", nargs="*")
args = parser.parse_args()
fastqc_dict = {"-o": "test", "-t": "2", "-k": "7", "": "FILENAME"}
fastqc_command = Command("fastqc")
fastqc_command.parse_params_dict(fastqc_dict)
print(fastqc_command)
update_fastqc_params = args.fastqc
updated_dict = update_params(fastqc_dict, update_fastqc_params)
fastqc_command.parse_params_dict(updated_dict)
print(updated_dict)