make requested changes to biweight

8 files changed, 71 insertions, 75 deletions

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)