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authorAlexander2022-05-28 20:15:39 +0300
committerBonfaceKilz2022-06-29 17:41:16 +0300
commit5d78eddfe974958bb90b3cc84bf8f8a78b568b01 (patch)
treef03d31d356ed59ff73fc2f72e9521ac9f06f1a22 /gn3
parent01f1af8f0c7149d8454b68d3cca25b9af50011da (diff)
downloadgenenetwork3-5d78eddfe974958bb90b3cc84bf8f8a78b568b01.tar.gz
parse output data
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/rust_correlation.py22
1 files changed, 21 insertions, 1 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index a3802ae..e739382 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -4,10 +4,30 @@ from gn3.settings import CORRELATION_COMMAND
from gn3.settings import TMPDIR
-def run_correlation(file_name: & str, outputdir: str = TMPDIR):
+def run_correlation(file_name: str, outputdir: str = TMPDIR):
command_list = [CORRELATION_COMMAND, file_name, outputdir]
results = subprocess.run(command_list, check=True)
return results
+
+
+def parse_correlation_output(result_file: str):
+
+ corr_results = []
+
+ with open(result_file, "r") 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