From d8c4b1a0188574cdd70638a99e2984b54bec6033 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 22:16:26 +0000
Subject: Fixed test_rqtl.py to include Rscript in the command

---
 tests/unit/computations/test_rqtl.py | 82 ++++++++++++++++++------------------
 1 file changed, 41 insertions(+), 41 deletions(-)

(limited to 'tests/unit/computations/test_rqtl.py')

diff --git a/tests/unit/computations/test_rqtl.py b/tests/unit/computations/test_rqtl.py
index b16f136..3bf8f81 100644
--- a/tests/unit/computations/test_rqtl.py
+++ b/tests/unit/computations/test_rqtl.py
@@ -1,41 +1,41 @@
-"""Test cases for procedures defined in computations.rqtl"""
-import unittest
-
-from unittest import mock
-from gn3.computations.rqtl import generate_rqtl_cmd
-
-class TestRqtl(unittest.TestCase):
-    """Test cases for computations.rqtl module"""
-    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
-    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
-    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
-        """Test computing mapping results with R/qtl"""
-        mock_get_hash_files.return_value = "my-hash1"
-        mock_generate_hash_string.return_value = "my-hash2"
-
-        self.assertEqual(
-            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
-                              rqtl_wrapper_kwargs={
-                                  "g": "genofile",
-                                  "p": "phenofile",
-                                  "model": "normal",
-                                  "method": "hk",
-                                  "nperm": 1000,
-                                  "scale": "Mb",
-                                  "control": "rs123456"
-                              },
-                              rqtl_wrapper_bool_kwargs=[
-                                  "addcovar",
-                                  "interval"
-                              ]), {
-                                  "output_file":
-                                  "my-hash1my-hash2my-hash2-output.json",
-                                  "rqtl_cmd": (
-                                      "rqtl-wrapper "
-                                      "--g genofile --p phenofile "
-                                      "--model normal --method hk "
-                                      "--nperm 1000 --scale Mb "
-                                      "--control rs123456 "
-                                      "--addcovar --interval"
-                                  )
-                              })
+"""Test cases for procedures defined in computations.rqtl"""
+import unittest
+
+from unittest import mock
+from gn3.computations.rqtl import generate_rqtl_cmd
+
+class TestRqtl(unittest.TestCase):
+    """Test cases for computations.rqtl module"""
+    @mock.patch("gn3.computations.rqtl.generate_hash_of_string")
+    @mock.patch("gn3.computations.rqtl.get_hash_of_files")
+    def test_generate_rqtl_command(self, mock_get_hash_files, mock_generate_hash_string):
+        """Test computing mapping results with R/qtl"""
+        mock_get_hash_files.return_value = "my-hash1"
+        mock_generate_hash_string.return_value = "my-hash2"
+
+        self.assertEqual(
+            generate_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper",
+                              rqtl_wrapper_kwargs={
+                                  "g": "genofile",
+                                  "p": "phenofile",
+                                  "model": "normal",
+                                  "method": "hk",
+                                  "nperm": 1000,
+                                  "scale": "Mb",
+                                  "control": "rs123456"
+                              },
+                              rqtl_wrapper_bool_kwargs=[
+                                  "addcovar",
+                                  "interval"
+                              ]), {
+                                  "output_file":
+                                  "my-hash1my-hash2my-hash2-output.json",
+                                  "rqtl_cmd": (
+                                      "Rscript rqtl-wrapper "
+                                      "--g genofile --p phenofile "
+                                      "--model normal --method hk "
+                                      "--nperm 1000 --scale Mb "
+                                      "--control rs123456 "
+                                      "--addcovar --interval"
+                                  )
+                              })
-- 
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