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authorAlexander_Kabui2022-07-21 23:26:52 +0300
committerBonfaceKilz2022-07-22 14:52:08 +0300
commitd4d1a39c4aa302ee2a074da6fdf76a6fab91c267 (patch)
treef47a95e184e6871a07925b8d9111bcdb28fb237a /gn3
parent5ad7a862dfa4d53fac9ddf7fd86075faa5167df5 (diff)
downloadgenenetwork3-d4d1a39c4aa302ee2a074da6fdf76a6fab91c267.tar.gz
compute num overlap
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/rust_correlation.py9
1 files changed, 6 insertions, 3 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index 4438d79..086db3b 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -89,10 +89,9 @@ def parse_correlation_output(result_file: str, top_n: int = 500) -> list[dict]:
lines = [next(file_reader) for x in range(top_n)]
for line in lines:
-
- (trait_name, corr_coeff, p_val) = line.rstrip().split(",")
+ (trait_name, corr_coeff, p_val, num_overlap) = line.rstrip().split(",")
corr_data = {
- "num_overlap": 00, # to be later fixed
+ "num_overlap": num_overlap,
"corr_coefficient": corr_coeff,
"p_value": p_val
}
@@ -169,3 +168,7 @@ def parse_tissue_corr_data(symbol_name: str,
pass
return (x_vals, data)
+
+
+def parse_lit_corr_data(trait, dataset):
+ pass