From fed7009b5eec9cc8b9370d4fb8486c7e4136b3d4 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 23 Jun 2021 10:18:54 +0300
Subject: minor fixes for biweight script

---
 gn3/computations/biweight.py | 10 ++++++----
 gn3/settings.py              |  2 +-
 scripts/calculate_biweight.R |  5 +++--
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
index 6d031ad..0377bdf 100644
--- a/gn3/computations/biweight.py
+++ b/gn3/computations/biweight.py
@@ -19,7 +19,9 @@ def calculate_biweight_corr(trait_vals: List,
     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)
+    try:
+        (corr_coeff, p_val) = tuple(
+            [float(y.strip()) for y in results.split()])
+        return (corr_coeff, p_val)
+    except Exception as e:
+        raise e
diff --git a/gn3/settings.py b/gn3/settings.py
index 770ba3d..f4866d5 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -23,4 +23,4 @@ SQLALCHEMY_TRACK_MODIFICATIONS = False
 GN2_BASE_URL = "http://www.genenetwork.org/"
 
 # biweight script
-BIWEIGHT_RSCRIPT = "~/genenetwork3/script/calculate_biweight.R"
+BIWEIGHT_RSCRIPT = "~/genenetwork3/scripts/calculate_biweight.R"
diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R
index bad93cb..8d8366e 100644
--- a/scripts/calculate_biweight.R
+++ b/scripts/calculate_biweight.R
@@ -13,7 +13,7 @@ ParseArgs <- function(args){
 }
 BiweightMidCorrelation <- function(trait_val,target_val){
 
-    results <- bicorAndPvalue(c(trait_val),c(target_val))
+    results <-bicorAndPvalue(as.numeric(unlist(trait_val)),as.numeric(unlist(target_val)))
     return ((c(c(results$bicor)[1],c(results$p)[1])))
 
 }
@@ -39,4 +39,5 @@ test_that("parsing args "),{
 
 parsed_values <- ParseArgs(arg_values)
 
-cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file
+
+cat(BiweightMidCorrelation(parsed_values[1],parsed_values[2]))
\ No newline at end of file
-- 
cgit v1.2.3