fix merge conflicts

5 files changed, 175 insertions, 145 deletions

diff --git a/tests/unit/computations/data/qtlreaper/main_output_sample.txt b/tests/unit/computations/data/qtlreaper/main_output_sample.txt
new file mode 100644
index 0000000..12b11b4
--- /dev/null
+++ b/tests/unit/computations/data/qtlreaper/main_output_sample.txt
@@ -0,0 +1,11 @@
+ID	Locus	Chr	cM	Mb	LRS	Additive	pValue
+T1	rs31443144	1	1.500	3.010	0.500	-0.074	1.000
+T1	rs6269442	1	1.500	3.492	0.500	-0.074	1.000
+T1	rs32285189	1	1.630	3.511	0.500	-0.074	1.000
+T1	rs258367496	1	1.630	3.660	0.500	-0.074	1.000
+T1	rs32430919	1	1.750	3.777	0.500	-0.074	1.000
+T1	rs36251697	1	1.880	3.812	0.500	-0.074	1.000
+T1	rs30658298	1	2.010	4.431	0.500	-0.074	1.000
+T1	rs51852623	1	2.010	4.447	0.500	-0.074	1.000
+T1	rs31879829	1	2.140	4.519	0.500	-0.074	1.000
+T1	rs36742481	1	2.140	4.776	0.500	-0.074	1.000
diff --git a/tests/unit/computations/data/qtlreaper/permu_output_sample.txt b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt
new file mode 100644
index 0000000..64cff07
--- /dev/null
+++ b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt
@@ -0,0 +1,27 @@
+4.44174
+5.03825
+5.08167
+5.18119
+5.18578
+5.24563
+5.24619
+5.24619
+5.27961
+5.28228
+5.43903
+5.50188
+5.51694
+5.56830
+5.63874
+5.71346
+5.71936
+5.74275
+5.76764
+5.79815
+5.81671
+5.82775
+5.89659
+5.92117
+5.93396
+5.93396
+5.94957
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py
deleted file mode 100644
index 650cb45..0000000
--- a/tests/unit/computations/test_heatmap.py
+++ /dev/null
@@ -1,143 +0,0 @@
-"""Module contains tests for gn3.computations.heatmap"""
-from unittest import TestCase
-from gn3.computations.heatmap import cluster_traits, export_trait_data
-
-strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
-trait_data = {
-    "mysqlid": 36688172,
-    "data": {
-        "B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
-        "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
-        "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
-        "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
-        "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
-        "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
-        "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
-        "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
-        "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
-        "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
-        "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
-        "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
-        "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
-        "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
-        "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
-        "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
-        "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
-        "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
-        "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
-        "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
-        "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
-        "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
-        "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
-        "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
-        "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
-        "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
-        "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
-
-class TestHeatmap(TestCase):
-    """Class for testing heatmap computation functions"""
-
-    def test_export_trait_data_dtype(self):
-        """
-        Test `export_trait_data` with different values for the `dtype` keyword
-        argument
-        """
-        for dtype, expected in [
-                ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["var", (None, None, None, None, None, None)],
-                ["N", (None, None, None, None, None, None)],
-                ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
-            with self.subTest(dtype=dtype):
-                self.assertEqual(
-                    export_trait_data(trait_data, strainlist, dtype=dtype),
-                    expected)
-
-    def test_export_trait_data_dtype_all_flags(self):
-        """
-        Test `export_trait_data` with different values for the `dtype` keyword
-        argument and the different flags set up
-        """
-        for dtype, vflag, nflag, expected in [
-                ["val", False, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", False, True,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", True, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["val", True, True,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["var", False, False, (None, None, None, None, None, None)],
-                ["var", False, True, (None, None, None, None, None, None)],
-                ["var", True, False, (None, None, None, None, None, None)],
-                ["var", True, True, (None, None, None, None, None, None)],
-                ["N", False, False, (None, None, None, None, None, None)],
-                ["N", False, True, (None, None, None, None, None, None)],
-                ["N", True, False, (None, None, None, None, None, None)],
-                ["N", True, True, (None, None, None, None, None, None)],
-                ["all", False, False,
-                 (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
-                ["all", False, True,
-                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
-                  8.30401, None, 7.80944, None)],
-                ["all", True, False,
-                 (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
-                  8.30401, None, 7.80944, None)],
-                ["all", True, True,
-                 (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
-                  8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
-        ]:
-            with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
-                self.assertEqual(
-                    export_trait_data(
-                        trait_data, strainlist, dtype=dtype, var_exists=vflag,
-                        n_exists=nflag),
-                    expected)
-
-    def test_cluster_traits(self):
-        """
-        Test that the clustering is working as expected.
-        """
-        traits_data_list = [
-            (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944),
-            (6.1427, 6.50588, 7.73705, 6.68328, 7.49293, 7.27398),
-            (8.4211, 8.30581, 9.24076, 8.51173, 9.18455, 8.36077),
-            (10.0904, 10.6509, 9.36716, 9.91202, 8.57444, 10.5731),
-            (10.188, 9.76652, 9.54813, 9.05074, 9.52319, 9.10505),
-            (6.74676, 7.01029, 7.54169, 6.48574, 7.01427, 7.26815),
-            (6.39359, 6.85321, 5.78337, 7.11141, 6.22101, 6.16544),
-            (6.84118, 7.08432, 7.59844, 7.08229, 7.26774, 7.24991),
-            (9.45215, 10.6943, 8.64719, 10.1592, 7.75044, 8.78615),
-            (7.04737, 6.87185, 7.58586, 6.92456, 6.84243, 7.36913)]
-        self.assertEqual(
-            cluster_traits(traits_data_list),
-            ((0.0, 0.20337048635536847, 0.16381088984330505, 1.7388553629398245,
-              1.5025235756329178, 0.6952839500255574, 1.271661230252733,
-              0.2100487290977544, 1.4699690641062024, 0.7934461515867415),
-             (0.20337048635536847, 0.0, 0.2198321044997198, 1.5753041735592204,
-              1.4815755944537086, 0.26087293140686374, 1.6939790104301427,
-              0.06024619831474998, 1.7430082449189215, 0.4497104244247795),
-             (0.16381088984330505, 0.2198321044997198, 0.0, 1.9073926868549234,
-              1.0396738891139845, 0.5278328671176757, 1.6275069061182947,
-              0.2636503792482082, 1.739617877037615, 0.7127042590637039),
-             (1.7388553629398245, 1.5753041735592204, 1.9073926868549234, 0.0,
-              0.9936846292920328, 1.1169999189889366, 0.6007483980555253,
-              1.430209221053372, 0.25879514152086425, 0.9313185954797953),
-             (1.5025235756329178, 1.4815755944537086, 1.0396738891139845,
-              0.9936846292920328, 0.0, 1.027827186339337, 1.1441743109173244,
-              1.4122477962364253, 0.8968250491499363, 1.1683723389247052),
-             (0.6952839500255574, 0.26087293140686374, 0.5278328671176757,
-              1.1169999189889366, 1.027827186339337, 0.0, 1.8420471110023269,
-              0.19179284676938602, 1.4875072385631605, 0.23451785425383564),
-             (1.271661230252733, 1.6939790104301427, 1.6275069061182947,
-              0.6007483980555253, 1.1441743109173244, 1.8420471110023269, 0.0,
-              1.6540234785929928, 0.2140799896286565, 1.7413442197913358),
-             (0.2100487290977544, 0.06024619831474998, 0.2636503792482082,
-              1.430209221053372, 1.4122477962364253, 0.19179284676938602,
-              1.6540234785929928, 0.0, 1.5225640692832796, 0.33370067057028485),
-             (1.4699690641062024, 1.7430082449189215, 1.739617877037615,
-              0.25879514152086425, 0.8968250491499363, 1.4875072385631605,
-              0.2140799896286565, 1.5225640692832796, 0.0, 1.3256191648260216),
-             (0.7934461515867415, 0.4497104244247795, 0.7127042590637039,
-              0.9313185954797953, 1.1683723389247052, 0.23451785425383564,
-              1.7413442197913358, 0.33370067057028485, 1.3256191648260216,
-              0.0)))
diff --git a/tests/unit/computations/test_parsers.py b/tests/unit/computations/test_parsers.py
index 19c3067..b51b0bf 100644
--- a/tests/unit/computations/test_parsers.py
+++ b/tests/unit/computations/test_parsers.py
@@ -15,7 +15,7 @@ class TestParsers(unittest.TestCase):
 
     def test_parse_genofile_with_existing_file(self):
         """Test that a genotype file is parsed correctly"""
-        strains = ["bxd1", "bxd2"]
+        samples = ["bxd1", "bxd2"]
         genotypes = [
             {"chr": "1", "locus": "rs31443144",
              "cm": "1.50", "mb": "3.010274",
@@ -51,4 +51,4 @@ class TestParsers(unittest.TestCase):
             "../test_data/genotype.txt"
         ))
         self.assertEqual(parse_genofile(
-            test_genotype_file), (strains, genotypes))
+            test_genotype_file), (samples, genotypes))
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
new file mode 100644
index 0000000..742d106
--- /dev/null
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -0,0 +1,135 @@
+"""Module contains tests for gn3.computations.qtlreaper"""
+from unittest import TestCase
+from gn3.computations.qtlreaper import (
+    parse_reaper_main_results,
+    organise_reaper_main_results,
+    parse_reaper_permutation_results)
+from tests.unit.sample_test_data import organised_trait_1
+
+class TestQTLReaper(TestCase):
+    """Class for testing qtlreaper interface functions."""
+
+    def test_parse_reaper_main_results(self):
+        """Test that the main results file is parsed correctly."""
+        self.assertEqual(
+            parse_reaper_main_results(
+                "tests/unit/computations/data/qtlreaper/main_output_sample.txt"),
+            [
+                {
+                    "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+                    "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+                    "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+                    "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+                    "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+                    "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+                    "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+                    "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs51852623", "Chr": 1, "cM": 2.010,
+                    "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs31879829", "Chr": 1, "cM": 2.140,
+                    "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs36742481", "Chr": 1, "cM": 2.140,
+                    "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                }
+            ])
+
+    def test_parse_reaper_permutation_results(self):
+        """Test that the permutations results file is parsed correctly."""
+        self.assertEqual(
+            parse_reaper_permutation_results(
+                "tests/unit/computations/data/qtlreaper/permu_output_sample.txt"),
+            [4.44174, 5.03825, 5.08167, 5.18119, 5.18578, 5.24563, 5.24619,
+             5.24619, 5.27961, 5.28228, 5.43903, 5.50188, 5.51694, 5.56830,
+             5.63874, 5.71346, 5.71936, 5.74275, 5.76764, 5.79815, 5.81671,
+             5.82775, 5.89659, 5.92117, 5.93396, 5.93396, 5.94957])
+
+    def test_organise_reaper_main_results(self):
+        """Check that results are organised correctly."""
+        self.assertEqual(
+            organise_reaper_main_results([
+                {
+                    "ID": "1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+                    "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+                    "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+                    "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+                    "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+                    "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+                    "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+                    "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+                    "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+                    "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+                    "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                }
+            ]),
+            organised_trait_1)