diff options
| -rw-r--r-- | gn3/computations/rust_correlation.py | 46 |
1 files changed, 44 insertions, 2 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index e739382..926e6fe 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -1,15 +1,57 @@ import subprocess +import json +from gn3.computations.qtlreaper import create_output_directory +from gn3.random import random_string from gn3.settings import CORRELATION_COMMAND from gn3.settings import TMPDIR -def run_correlation(file_name: str, outputdir: str = TMPDIR): +def generate_input_files(dataset: list[str], output_dir: str = TMPDIR): + """function generates outputfiles and inputfiles""" - command_list = [CORRELATION_COMMAND, file_name, outputdir] + tmpdir = create_output_directory(f"{output_dir}/correlation") + + tmp_file = os.path.join(tmpdir, f"/{random_string(10)}.txt") + + with open(tmp_file, "w") as file_writer: + 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_json_file = os.path.join(tmp_dir, f"/{random_string(10)}.json") + + correlation_args = { + "method": kwargs.get("method", "pearson"), + "file_path": tmp_file, + "x_vals": kwargs.get("x_vals"), + "file_delimiter": kwargs.get("delimiter", ",") + } + + with open(tmp_json_file, "w") as outputfile: + json.dump(correlation_args, outputfile) + + return tmp_json_file + + +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}) + + command_list = [CORRELATION_COMMAND, generate_json_file, outputdir] results = subprocess.run(command_list, check=True) + # handle errors + return results |