From d086881ae5b97cd5ac0a5a5d55a5f4a6f9d83896 Mon Sep 17 00:00:00 2001
From: Alexander
Date: Wed, 1 Jun 2022 21:03:34 +0300
Subject: minor fixes
---
gn3/computations/rust_correlation.py | 22 ++++++++++++----------
1 file changed, 12 insertions(+), 10 deletions(-)
(limited to 'gn3')
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
--
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