diff options
| -rw-r--r-- | gn3/computations/rust_correlation.py | 22 |
1 files changed, 12 insertions, 10 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index 926e6fe..2837138 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -1,5 +1,7 @@ import subprocess import json +import os + from gn3.computations.qtlreaper import create_output_directory from gn3.random import random_string @@ -10,22 +12,24 @@ from gn3.settings import TMPDIR def generate_input_files(dataset: list[str], output_dir: str = TMPDIR): """function generates outputfiles and inputfiles""" - tmpdir = create_output_directory(f"{output_dir}/correlation") + tmp_dir = f"{output_dir}/correlation" + + create_output_directory(tmp_dir) - tmp_file = os.path.join(tmpdir, f"/{random_string(10)}.txt") + tmp_file = os.path.join(tmp_dir, f"{random_string(10)}.txt") with open(tmp_file, "w") as file_writer: - file_writer.write("\n".join(dataset)) + file_writer.write("\n".join(dataset)) return (tmp_dir, tmp_file) def generate_json_file(**kwargs): """generating json input file required by cargo""" - (tmp_dir, tmp_file) = generate_json_file(kwargs.get("dataset")) + (tmp_dir, tmp_file) = (kwargs.get("tmp_dir"), kwargs.get("tmp_file")) - tmp_json_file = os.path.join(tmp_dir, f"/{random_string(10)}.json") + tmp_json_file = os.path.join(tmp_dir, f"{random_string(10)}.json") correlation_args = { "method": kwargs.get("method", "pearson"), @@ -43,15 +47,13 @@ def generate_json_file(**kwargs): def run_correlation(dataset, trait_vals: list[str], method: str, delimiter: str): """entry function to call rust correlation""" - generate_json_file = generate_json_file( - {"method": method, "delimiter": delimiter, "x_vals": trait_vals}) + json_file = generate_json_file(** + {"method": method, "delimiter": delimiter, "x_vals": trait_vals}) - command_list = [CORRELATION_COMMAND, generate_json_file, outputdir] + command_list = [CORRELATION_COMMAND, json_file, outputdir] results = subprocess.run(command_list, check=True) - # handle errors - return results |