diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/rust_correlation.py | 26 |
1 files changed, 20 insertions, 6 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index 2837138..c2783f1 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -1,3 +1,9 @@ +"""module contains code integration correlation implemented in rust here + +https://github.com/Alexanderlacuna/correlation_rust + +""" + import subprocess import json import os @@ -18,7 +24,7 @@ def generate_input_files(dataset: list[str], output_dir: str = TMPDIR): tmp_file = os.path.join(tmp_dir, f"{random_string(10)}.txt") - with open(tmp_file, "w") as file_writer: + with open(tmp_file, "w", encoding="utf-8") as file_writer: file_writer.write("\n".join(dataset)) return (tmp_dir, tmp_file) @@ -38,19 +44,26 @@ def generate_json_file(**kwargs): "file_delimiter": kwargs.get("delimiter", ",") } - with open(tmp_json_file, "w") as outputfile: + with open(tmp_json_file, "w", encoding="utf-8") as outputfile: json.dump(correlation_args, outputfile) return tmp_json_file -def run_correlation(dataset, trait_vals: list[str], method: str, delimiter: str): +def run_correlation(dataset, trait_vals: + list[str], + method: str, + delimiter: str): """entry function to call rust correlation""" + (tmp_dir, tmp_file) = generate_input_files(dataset) + json_file = generate_json_file(** - {"method": method, "delimiter": delimiter, "x_vals": trait_vals}) + {"tmp_dir": tmp_dir, "tmp_file": tmp_file, + "method": method, "delimiter": delimiter, + "x_vals": trait_vals}) - command_list = [CORRELATION_COMMAND, json_file, outputdir] + command_list = [CORRELATION_COMMAND, json_file, TMPDIR] results = subprocess.run(command_list, check=True) @@ -58,10 +71,11 @@ def run_correlation(dataset, trait_vals: list[str], method: str, delimiter: str) def parse_correlation_output(result_file: str): + """parse file output """ corr_results = [] - with open(result_file, "r") as file_reader: + with open(result_file, "r", encoding="utf-8") as file_reader: for line in file_reader: |