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authorAlexander_Kabui2022-07-28 19:30:59 +0300
committerFrederick Muriuki Muriithi2022-08-10 09:23:16 +0300
commit69ab1d5dfa04fbff326df35349c55fc9b4d31f2a (patch)
tree943f68fc6dca66c8088e95954ac53f7d40c13a32 /gn3
parentf6d9b2fba94ae363846df0b5ecd619c192d7d2bf (diff)
downloadgenenetwork3-69ab1d5dfa04fbff326df35349c55fc9b4d31f2a.tar.gz
enhancements for rust tissue
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/rust_correlation.py32
1 files changed, 23 insertions, 9 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index 07e0e56..db357fe 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -45,7 +45,9 @@ def generate_json_file(
return (output_file, tmp_json_file)
-def run_correlation(dataset, trait_vals: str, method: str, delimiter: str):
+def run_correlation(
+ dataset, trait_vals: str, method: str, delimiter: str,
+ corr_type: str = "sample", top_n: int = 500):
"""entry function to call rust correlation"""
(tmp_dir, tmp_file) = generate_input_files(dataset)
(output_file, json_file) = generate_json_file(
@@ -53,19 +55,31 @@ def run_correlation(dataset, trait_vals: str, method: str, delimiter: str):
x_vals=trait_vals)
command_list = [CORRELATION_COMMAND, json_file, TMPDIR]
subprocess.run(command_list, check=True)
- return parse_correlation_output(output_file, 500)
+ return parse_correlation_output(output_file, corr_type, top_n)
-def parse_correlation_output(result_file: str, top_n: int = 500) -> list[dict]:
+
+def parse_correlation_output(result_file: str,
+ corr_type: str, top_n: int = 500) -> dict:
"""parse file output """
def __parse_line__(line):
(trait_name, corr_coeff, p_val, num_overlap) = line.rstrip().split(",")
- return {
- trait_name: {
- "num_overlap": num_overlap,
- "corr_coefficient": corr_coeff,
- "p_value": p_val
- }}
+ if corr_type == "sample":
+ return {
+ trait_name: {
+ "num_overlap": num_overlap,
+ "corr_coefficient": corr_coeff,
+ "p_value": p_val
+ }
+ }
+ if corr_type == "tissue":
+ return {
+ trait_name: {
+ "tissue_corr": corr_coeff,
+ "tissue_number": num_overlap,
+ "tissue_p_val": p_val
+ }
+ }
with open(result_file, "r", encoding="utf-8") as file_reader:
return [