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authorAlexander2022-06-15 22:45:29 +0300
committerBonfaceKilz2022-06-29 17:41:16 +0300
commite7347aca4c3cb02c5febb915f4fb1dd5cda46ec0 (patch)
tree8c190610811a16282740bffa14de7b092618f76a
parent74cfc8ec86afceba0fe83e0e49c5be08db4ff065 (diff)
downloadgenenetwork3-e7347aca4c3cb02c5febb915f4fb1dd5cda46ec0.tar.gz
pylint fixes
-rw-r--r--gn3/computations/rust_correlation.py26
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: