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"""module contains code integration correlation implemented in rust here
https://github.com/Alexanderlacuna/correlation_rust
"""
import subprocess
import json
import os
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 generate_input_files(dataset: list[str],
output_dir: str = TMPDIR) ->(str, str):
"""function generates outputfiles and inputfiles"""
tmp_dir = f"{output_dir}/correlation"
create_output_directory(tmp_dir)
tmp_file = os.path.join(tmp_dir, f"{random_string(10)}.txt")
with open(tmp_file, "w", encoding="utf-8") 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) = (kwargs.get("tmp_dir"), kwargs.get("tmp_file"))
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", 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):
"""entry function to call rust correlation"""
(tmp_dir, tmp_file) = generate_input_files(dataset)
json_file = generate_json_file(**
{"tmp_dir": tmp_dir, "tmp_file": tmp_file,
"method": method, "delimiter": delimiter,
"x_vals": trait_vals})
command_list = [CORRELATION_COMMAND, json_file, TMPDIR]
return subprocess.run(command_list, check=True)
def parse_correlation_output(result_file: str):
"""parse file output """
corr_results = []
with open(result_file, "r", encoding="utf-8") as file_reader:
for line in file_reader:
(trait_name, corr_coeff, p_val) = line.rstrip().split(",")
corr_data = {
"trait_name": trait_name,
"corr_coeff": corr_coeff,
"p_val": p_val
}
corr_results.append(corr_data)
return corr_results
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