Provide function to organise parsed QTLReaper results

* gn3/computations/qtlreaper.py: Provide a function to organise the results by
  trait for easier use down the line.

* tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the
  organising function works as expected.

1 files changed, 104 insertions, 1 deletions

diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index fd3434a..1d7347f 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -1,7 +1,9 @@
 """Module contains tests for gn3.computations.qtlreaper"""
 from unittest import TestCase
 from gn3.computations.qtlreaper import (
-    parse_reaper_main_results, parse_reaper_permutation_results)
+    parse_reaper_main_results,
+    organise_reaper_main_results,
+    parse_reaper_permutation_results)
 
 class TestQTLReaper(TestCase):
     """Class for testing qtlreaper interface functions."""
@@ -73,3 +75,104 @@ class TestQTLReaper(TestCase):
              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):
+        self.assertEqual(
+            organise_reaper_main_results([
+                {
+                    "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": 2, "cM": 2.010,
+                    "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+                    "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                },
+                {
+                    "ID": "T1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+                    "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+                    "pValue": 1.000
+                }
+            ]),
+            [{"ID": "T1",
+              "chromosomes": [
+                  {"Chr": "1",
+                   "loci": [
+                       {
+                           "Locus": "rs31443144",  "cM": 1.500, "Mb": 3.010,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       }]},
+                  {"Chr": "2",
+                   "loci": [
+                       {
+                           "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       },
+                       {
+                           "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+                           "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+                       }]}]}])