From 57a6af689e85e5cbfe0a825d5b84ed9c451e6ad7 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 13:36:40 +0300
Subject: add biweight r script and tests

---
 gn3/computations/biweight.R                 | 15 +++++++++++++++
 gn3/computations/biweight.py                | 22 ++++++++++++++++++++++
 gn3/computations/correlations.py            | 10 ++++++++--
 tests/unit/computations/test_biweight.py    | 21 +++++++++++++++++++++
 tests/unit/computations/test_correlation.py |  6 ++++--
 5 files changed, 70 insertions(+), 4 deletions(-)
 create mode 100644 gn3/computations/biweight.R
 create mode 100644 gn3/computations/biweight.py
 create mode 100644 tests/unit/computations/test_biweight.py

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
new file mode 100644
index 0000000..d0d8de4
--- /dev/null
+++ b/gn3/computations/biweight.R
@@ -0,0 +1,15 @@
+
+library(WGCNA)
+
+
+myArgs <- commandArgs(trailingOnly = TRUE)
+trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
+target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
+
+BiweightMidCorrelation <- function(trait_val,target_val){
+    # results <- bicorAndPvalue(x,y)
+    return (list(c(results$bicor)[1],c(results$p)[1]))
+}
+cat(BiweightMidCorrelation(trait_vals,target_vals))
+
+
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
new file mode 100644
index 0000000..c17de8e
--- /dev/null
+++ b/gn3/computations/biweight.py
@@ -0,0 +1,22 @@
+
+
+"""module contains script to call biweight mid\
+correlation in R"""
+
+import subprocess
+from typing import List
+
+
+def call_biweight_script(trait_vals: List,
+                         target_vals: List,
+                         path_to_script: str = "./biweight_R",
+                         command: str = "Rscript"
+                         ):
+    '''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)
+
+    return tuple([float(y) for y in results.split()])
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index f0ce502..89d37fc 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -7,6 +7,7 @@ from typing import Optional
 from typing import Callable
 
 import scipy.stats
+from gn3.computations.biweight import call_biweight_script
 
 
 def map_shared_keys_to_values(target_sample_keys: List,
@@ -99,8 +100,13 @@ def do_bicor(x_val, y_val) -> Tuple[float, float]:
 package :not packaged in guix
 
     """
-    x_val, y_val = 0, 0
-    return (x_val, y_val)
+
+    try:
+        results = call_biweight_script(x_val, y_val)
+    except Exception as error:
+        raise error
+
+    return results
 
 
 def filter_shared_sample_keys(this_samplelist,
diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py
new file mode 100644
index 0000000..3045f78
--- /dev/null
+++ b/tests/unit/computations/test_biweight.py
@@ -0,0 +1,21 @@
+"""test for biweight script"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.computations.biweight import call_biweight_script
+
+
+class TestBiweight(TestCase):
+    """test class for biweight"""
+
+    @mock.patch("gn3.computations.biweight.subprocess.check_output")
+    def test_call_biweight_script(self, mock_check_output):
+        """test for call_biweight_script func"""
+        mock_check_output.return_value = "0.1 0.5"
+        results = call_biweight_script(command="Rscript",
+                                       path_to_script="./r_script.R",
+                                       trait_vals=[
+                                           1.2, 1.1, 1.9],
+                                       target_vals=[1.9, 0.4, 1.1])
+
+        self.assertEqual(results, (0.1, 0.5))
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 5746adf..606f96d 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -98,12 +98,14 @@ class TestCorrelation(TestCase):
 
         self.assertEqual(results, expected_results)
 
-    def test_bicor(self):
+    @mock.patch("gn3.computations.correlations.call_biweight_script")
+    def test_bicor(self, mock_biweight):
         """Test for doing biweight mid correlation """
+        mock_biweight.return_value = (1.0, 0.0)
 
         results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6])
 
-        self.assertEqual(results, (0.0, 0.0)
+        self.assertEqual(results, (1.0, 0.0)
                          )
 
     @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
-- 
cgit v1.2.3


From f9dec15fb4a1fc24dfb963ed69f2a5cbbd4f31d3 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 13:50:21 +0300
Subject: fix missing call to bicorAndPvalue

---
 gn3/computations/biweight.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index d0d8de4..05f7145 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -7,7 +7,7 @@ trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
 target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
 
 BiweightMidCorrelation <- function(trait_val,target_val){
-    # results <- bicorAndPvalue(x,y)
+    results <- bicorAndPvalue(x,y)
     return (list(c(results$bicor)[1],c(results$p)[1]))
 }
 cat(BiweightMidCorrelation(trait_vals,target_vals))
-- 
cgit v1.2.3


From c708f435f14e5394aa4e6e8f556aec976d61341f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 15 Jun 2021 08:08:38 +0300
Subject: fix script path issues

---
 gn3/computations/biweight.R  | 19 ++++++++++++++++---
 gn3/computations/biweight.py |  8 ++++++--
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index 05f7145..650c5fd 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -1,5 +1,5 @@
 
-library(WGCNA)
+# library(WGCNA)
 
 
 myArgs <- commandArgs(trailingOnly = TRUE)
@@ -7,9 +7,22 @@ trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
 target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
 
 BiweightMidCorrelation <- function(trait_val,target_val){
-    results <- bicorAndPvalue(x,y)
+    results <- bicorAndPvalue(trait_val,target_val)
     return (list(c(results$bicor)[1],c(results$p)[1]))
 }
-cat(BiweightMidCorrelation(trait_vals,target_vals))
 
 
+
+
+
+
+# the idea is that you get the entire dataset in any format 
+# and then do ther correlation
+
+ComputeAll <-function(trait_val,target_dataset) {
+	for target_val in target_dataset {
+      results = BiweightMidCorrelation(trait_val,target_val)
+      cat(BiweightMidCorrelation(trait_vals,target_vals))
+	}
+}
+
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
index c17de8e..e598a5b 100644
--- a/gn3/computations/biweight.py
+++ b/gn3/computations/biweight.py
@@ -2,17 +2,21 @@
 
 """module contains script to call biweight mid\
 correlation in R"""
-
 import subprocess
+import os
+from pathlib import Path
 from typing import List
 
+FILE_PATH = os.path.join(Path(__file__).parent.absolute(), "biweight.R")
+
 
 def call_biweight_script(trait_vals: List,
                          target_vals: List,
-                         path_to_script: str = "./biweight_R",
+                         path_to_script: str = FILE_PATH,
                          command: str = "Rscript"
                          ):
     '''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]
-- 
cgit v1.2.3


From 88e3bd10a2481e6c00c454a6bf2c60448ada363c Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Jun 2021 08:44:56 +0300
Subject: add fetch args function

---
 gn3/computations/biweight.R | 31 ++++++++++++-------------------
 1 file changed, 12 insertions(+), 19 deletions(-)

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index 650c5fd..8730536 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -1,28 +1,21 @@
 
-# library(WGCNA)
+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=" ")))
 
-myArgs <- commandArgs(trailingOnly = TRUE)
-trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
-target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
+	return(list(trait_vals= c(trait_vals),target_vals = c(target_vals)))
 
-BiweightMidCorrelation <- function(trait_val,target_val){
-    results <- bicorAndPvalue(trait_val,target_val)
-    return (list(c(results$bicor)[1],c(results$p)[1]))
 }
+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]))
 
-
-
-# the idea is that you get the entire dataset in any format 
-# and then do ther correlation
-
-ComputeAll <-function(trait_val,target_dataset) {
-	for target_val in target_dataset {
-      results = BiweightMidCorrelation(trait_val,target_val)
-      cat(BiweightMidCorrelation(trait_vals,target_vals))
-	}
-}
-
+cat(results)
\ No newline at end of file
-- 
cgit v1.2.3


From ceaea7930b0205993b9357bd1317fefe0c51b3b6 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Jun 2021 13:39:39 +0300
Subject: add r_testthatpackage

---
 guix.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/guix.scm b/guix.scm
index 75084db..bf700d0 100644
--- a/guix.scm
+++ b/guix.scm
@@ -30,6 +30,7 @@
  (gnu packages cran)
  (gnu packages databases)
  (gnu packages statistics)
+ (gnu packages bioconductor)
  (gnu packages python)
  (gnu packages python-check)
  (gnu packages python-crypto)
@@ -86,6 +87,7 @@
                        ("r" ,r)
                        ; ("r-ctl" ,r-ctl)
                        ("r-qtl" ,r-qtl)
+                       ("r-testthat" ,r-testthat)
                        ("r-optparse" ,r-optparse)
                        ; ("r-wgcna" ,r-wgcna)
                        ))
-- 
cgit v1.2.3


From c0931bda121c1b39e1ae2adc7bfa49c2ca207a4d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Jun 2021 13:41:28 +0300
Subject: refactor script and add tests

---
 gn3/computations/biweight.R      | 14 ++++++++------
 gn3/computations/test_biweight.R | 28 ++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 6 deletions(-)
 create mode 100644 gn3/computations/test_biweight.R

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
-- 
cgit v1.2.3


From bc7d84077a3e99f8fd54f2e0050ac4bad8a36b01 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Jun 2021 14:03:28 +0300
Subject: minor fix

---
 gn3/computations/test_biweight.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gn3/computations/test_biweight.R b/gn3/computations/test_biweight.R
index 149c8b6..2269120 100644
--- a/gn3/computations/test_biweight.R
+++ b/gn3/computations/test_biweight.R
@@ -7,9 +7,6 @@ test_that("sum of vector", {
 })
 
 
-
-test
-
 test_that("biweight results"),{
 	vec_1 = c(1,2,3,4)
 	vec_2 = c(1,2,3,4)
-- 
cgit v1.2.3


From b566a8950864a373f95ae2914b862e9846297b2d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Jun 2021 14:07:24 +0300
Subject: add r-wgna package

---
 gn3/computations/test_biweight.R | 8 ++++----
 guix.scm                         | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/gn3/computations/test_biweight.R b/gn3/computations/test_biweight.R
index 2269120..599e733 100644
--- a/gn3/computations/test_biweight.R
+++ b/gn3/computations/test_biweight.R
@@ -8,16 +8,16 @@ test_that("sum of vector", {
 
 
 test_that("biweight results"),{
-	vec_1 = c(1,2,3,4)
-	vec_2 = c(1,2,3,4)
+	vec_1 <- c(1,2,3,4)
+	vec_2 <- c(1,2,3,4)
 
-	results = BiweightMidCorrelation(vec_1,vec_2)
+	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")
+	my_args <- c("1 2 3 4","5 6 7 8")
 	results <- ParseArgs(my_args)
 
 	expect_equal(results[1],c(1,2,3,4))
diff --git a/guix.scm b/guix.scm
index bf700d0..d41600d 100644
--- a/guix.scm
+++ b/guix.scm
@@ -89,7 +89,7 @@
                        ("r-qtl" ,r-qtl)
                        ("r-testthat" ,r-testthat)
                        ("r-optparse" ,r-optparse)
-                       ; ("r-wgcna" ,r-wgcna)
+                       ("r-wgcna" ,r-wgcna)
                        ))
   (build-system python-build-system)
   (home-page "https://github.com/genenetwork/genenetwork3")
-- 
cgit v1.2.3


From 864f231bbdbe2c3b3c96b0158a15811ac7790c3f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 20 Jun 2021 09:04:55 +0300
Subject: make requested  changes to biweight

---
 gn3/computations/biweight.R                 | 23 ----------------
 gn3/computations/biweight.py                | 25 +++++++++--------
 gn3/computations/correlations.py            |  7 +++--
 gn3/computations/test_biweight.R            | 25 -----------------
 gn3/settings.py                             |  6 ++++-
 scripts/calculate_biweight.R                | 42 +++++++++++++++++++++++++++++
 tests/unit/computations/test_biweight.py    | 16 +++++------
 tests/unit/computations/test_correlation.py |  2 +-
 8 files changed, 71 insertions(+), 75 deletions(-)
 delete mode 100644 gn3/computations/biweight.R
 delete mode 100644 gn3/computations/test_biweight.R
 create mode 100644 scripts/calculate_biweight.R

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
deleted file mode 100644
index e424360..0000000
--- a/gn3/computations/biweight.R
+++ /dev/null
@@ -1,23 +0,0 @@
-
-library(WGCNA)
-
-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)))
-
-}
-BiweightMidCorrelation <- function(trait_val,target_val){
-
-	results <- bicorAndPvalue(c(trait_val),c(target_val))
-    return ((c(c(results$bicor)[1],c(results$p)[1])))
-
-}
-
-
-parsed_values <- ParseArgs(arg_values)
-
-cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file
diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
index e598a5b..f5eecb2 100644
--- a/gn3/computations/biweight.py
+++ b/gn3/computations/biweight.py
@@ -1,20 +1,17 @@
-
-
-"""module contains script to call biweight mid\
-correlation in R"""
+"""module contains script to call biweight midcorrelation in R"""
 import subprocess
-import os
-from pathlib import Path
+
 from typing import List
+from typing import Tuple
 
-FILE_PATH = os.path.join(Path(__file__).parent.absolute(), "biweight.R")
+from gn3.settings import BIWEIGHT_RSCRIPT
 
 
-def call_biweight_script(trait_vals: List,
-                         target_vals: List,
-                         path_to_script: str = FILE_PATH,
-                         command: str = "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)
@@ -23,4 +20,6 @@ def call_biweight_script(trait_vals: List,
 
     results = subprocess.check_output(cmd, universal_newlines=True)
 
-    return tuple([float(y) for y in results.split()])
+    (corr_coeff, p_val) = tuple([float(y) for y in results.split()])
+
+    return (corr_coeff, p_val)
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index 89d37fc..eae7ae4 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -7,7 +7,7 @@ from typing import Optional
 from typing import Callable
 
 import scipy.stats
-from gn3.computations.biweight import call_biweight_script
+from gn3.computations.biweight import calculate_biweight_corr
 
 
 def map_shared_keys_to_values(target_sample_keys: List,
@@ -102,12 +102,11 @@ package :not packaged in guix
     """
 
     try:
-        results = call_biweight_script(x_val, y_val)
+        results = calculate_biweight_corr(x_val, y_val)
+        return results
     except Exception as error:
         raise error
 
-    return results
-
 
 def filter_shared_sample_keys(this_samplelist,
                               target_samplelist) -> Tuple[List, List]:
diff --git a/gn3/computations/test_biweight.R b/gn3/computations/test_biweight.R
deleted file mode 100644
index 599e733..0000000
--- a/gn3/computations/test_biweight.R
+++ /dev/null
@@ -1,25 +0,0 @@
-library(testthat)
-source("./biweight.R", chdir = TRUE)
-
-test_that("sum of vector", {
-  results <- sum(c(1,2))
-  expect_equal(results, 3)
-})
-
-
-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
diff --git a/gn3/settings.py b/gn3/settings.py
index 2057ce1..bde856d 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -13,9 +13,13 @@ TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())
 RQTL_WRAPPER = "rqtl_wrapper.R"
 
 # SQL confs
-SQL_URI = os.environ.get("SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl")
+SQL_URI = os.environ.get(
+    "SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl")
 SECRET_KEY = "password"
 SQLALCHEMY_TRACK_MODIFICATIONS = False
 # gn2 results only used in fetching dataset info
 
 GN2_BASE_URL = "http://www.genenetwork.org/"
+
+# biweight script
+BIWEIGHT_RSCRIPT = "~/genenetwork3/script/calculate_biweight.R"
diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R
new file mode 100644
index 0000000..bad93cb
--- /dev/null
+++ b/scripts/calculate_biweight.R
@@ -0,0 +1,42 @@
+
+library(testthat)
+library(WGCNA)
+
+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)))
+
+}
+BiweightMidCorrelation <- function(trait_val,target_val){
+
+    results <- bicorAndPvalue(c(trait_val),c(target_val))
+    return ((c(c(results$bicor)[1],c(results$p)[1])))
+
+}
+
+
+
+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))
+}
+
+parsed_values <- ParseArgs(arg_values)
+
+cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
\ No newline at end of file
diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py
index 3045f78..ad404f1 100644
--- a/tests/unit/computations/test_biweight.py
+++ b/tests/unit/computations/test_biweight.py
@@ -2,20 +2,20 @@
 from unittest import TestCase
 from unittest import mock
 
-from gn3.computations.biweight import call_biweight_script
+from gn3.computations.biweight import calculate_biweight_corr
 
 
 class TestBiweight(TestCase):
     """test class for biweight"""
 
     @mock.patch("gn3.computations.biweight.subprocess.check_output")
-    def test_call_biweight_script(self, mock_check_output):
-        """test for call_biweight_script func"""
+    def test_calculate_biweight_corr(self, mock_check_output):
+        """test for calculate_biweight_corr func"""
         mock_check_output.return_value = "0.1 0.5"
-        results = call_biweight_script(command="Rscript",
-                                       path_to_script="./r_script.R",
-                                       trait_vals=[
-                                           1.2, 1.1, 1.9],
-                                       target_vals=[1.9, 0.4, 1.1])
+        results = calculate_biweight_corr(command="Rscript",
+                                          path_to_script="./r_script.R",
+                                          trait_vals=[
+                                              1.2, 1.1, 1.9],
+                                          target_vals=[1.9, 0.4, 1.1])
 
         self.assertEqual(results, (0.1, 0.5))
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 606f96d..b1bc6ef 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -98,7 +98,7 @@ class TestCorrelation(TestCase):
 
         self.assertEqual(results, expected_results)
 
-    @mock.patch("gn3.computations.correlations.call_biweight_script")
+    @mock.patch("gn3.computations.correlations.calculate_biweight_corr")
     def test_bicor(self, mock_biweight):
         """Test for doing biweight mid correlation """
         mock_biweight.return_value = (1.0, 0.0)
-- 
cgit v1.2.3


From 75801d83c8302b48051d413490e6ce2a0b8ff01f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 20 Jun 2021 09:09:01 +0300
Subject: fix conflict

---
 guix.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/guix.scm b/guix.scm
index d41600d..104dc51 100644
--- a/guix.scm
+++ b/guix.scm
@@ -87,8 +87,10 @@
                        ("r" ,r)
                        ; ("r-ctl" ,r-ctl)
                        ("r-qtl" ,r-qtl)
-                       ("r-testthat" ,r-testthat)
                        ("r-optparse" ,r-optparse)
+                       ("r-stringi" ,r-stringi)
+                       ("r-stringr" ,r-stringr)
+                       ("r-testthat" ,r-testthat)
                        ("r-wgcna" ,r-wgcna)
                        ))
   (build-system python-build-system)
-- 
cgit v1.2.3


From 10140ab707021dd2dffb1b439f52a62e3d59c29a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 20 Jun 2021 09:15:00 +0300
Subject: minor fix docstring

---
 gn3/computations/biweight.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py
index f5eecb2..6d031ad 100644
--- a/gn3/computations/biweight.py
+++ b/gn3/computations/biweight.py
@@ -12,7 +12,7 @@ def calculate_biweight_corr(trait_vals: List,
                             path_to_script: str = BIWEIGHT_RSCRIPT,
                             command: str = "Rscript"
                             ) -> Tuple[float, float]:
-    '''biweight function'''
+    """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)
-- 
cgit v1.2.3