Merge pull request #20 from genenetwork/feature/biweight-correlation

add biweight r script and tests

1 files changed, 25 insertions, 0 deletions

diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
new file mode 100644
index 0000000..6d031ad
--- /dev/null
+++ b/gn3/computations/biweight.py
@@ -0,0 +1,25 @@
+"""module contains script to call biweight midcorrelation in R"""
+import subprocess
+
+from typing import List
+from typing import Tuple
+
+from gn3.settings import BIWEIGHT_RSCRIPT
+
+
+def calculate_biweight_corr(trait_vals: List,
+                            target_vals: List,
+                            path_to_script: str = BIWEIGHT_RSCRIPT,
+                            command: str = "Rscript"
+                            ) -> Tuple[float, float]:
+    """biweight function"""
+
+    args_1 = ' '.join(str(trait_val) for trait_val in trait_vals)
+    args_2 = ' '.join(str(target_val) for target_val in target_vals)
+    cmd = [command, path_to_script] + [args_1] + [args_2]
+
+    results = subprocess.check_output(cmd, universal_newlines=True)
+
+    (corr_coeff, p_val) = tuple([float(y) for y in results.split()])
+
+    return (corr_coeff, p_val)