refactor script and add tests

2 files changed, 36 insertions, 6 deletions

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index 8730536..e424360 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -1,10 +1,11 @@
 
 library(WGCNA)
 
-FetchArgs <- function(){
-	myArgs <- commandArgs(trailingOnly = TRUE)
-	trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
-	target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
+arg_values <- commandArgs(trailingOnly = TRUE)
+ParseArgs <- function(args){
+
+	trait_vals <- as.numeric(unlist(strsplit(args[1], split=" ")))
+	target_vals <- as.numeric(unlist(strsplit(args[2], split=" ")))
 
 	return(list(trait_vals= c(trait_vals),target_vals = c(target_vals)))
 
@@ -13,9 +14,10 @@ BiweightMidCorrelation <- function(trait_val,target_val){
 
 	results <- bicorAndPvalue(c(trait_val),c(target_val))
     return ((c(c(results$bicor)[1],c(results$p)[1])))
+
 }
 
 
-results <- (BiweightMidCorrelation(FetchArgs()[1],FetchArgs()[2]))
+parsed_values <- ParseArgs(arg_values)
 
-cat(results)
\ No newline at end of file
+cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file
diff --git a/gn3/computations/test_biweight.R b/gn3/computations/test_biweight.R
new file mode 100644
index 0000000..149c8b6
--- /dev/null
+++ b/gn3/computations/test_biweight.R
@@ -0,0 +1,28 @@
+library(testthat)
+source("./biweight.R", chdir = TRUE)
+
+test_that("sum of vector", {
+  results <- sum(c(1,2))
+  expect_equal(results, 3)
+})
+
+
+
+test
+
+test_that("biweight results"),{
+	vec_1 = c(1,2,3,4)
+	vec_2 = c(1,2,3,4)
+
+	results = BiweightMidCorrelation(vec_1,vec_2)
+	expect_equal(c(1.0,0.0),results)
+}
+
+
+test_that("parsing args "),{
+	my_args = c("1 2 3 4","5 6 7 8")
+	results <- ParseArgs(my_args)
+
+	expect_equal(results[1],c(1,2,3,4))
+	expect_equal(results[2],c(5,6,7,8))
+}
\ No newline at end of file