From a718069c757bea9f7ecbaee25e23bd581750f906 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Wed, 8 Sep 2021 10:56:56 +0300
Subject: Ease search for traits and chromosomes

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* Return a dict of values rather than list for the traits and chromosomes to
  ease searching through the data.
---
 gn3/computations/qtlreaper.py             |  9 ++-
 tests/unit/computations/test_qtlreaper.py | 92 +++++++++++++++----------------
 2 files changed, 52 insertions(+), 49 deletions(-)

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 02d6572..5180853 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -110,12 +110,15 @@ def organise_reaper_main_results(parsed_results):
         unique_chromosomes = {item["Chr"] for item in id_items}
         return {
             "ID": identifier,
-            "chromosomes": [
+            "chromosomes": {_chr["Chr"]: _chr for _chr in [
                 __organise_by_chromosome(chromo, id_items)
-                for chromo in sorted(unique_chromosomes)]}
+                for chromo in sorted(
+                        unique_chromosomes, key=chromosome_sorter_key_fn)]}}
 
     unique_ids = {res["ID"] for res in parsed_results}
-    return [__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)]
+    return {
+        trait["ID"]: trait for trait in
+        [__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)]}
 
 def parse_reaper_main_results(results_file):
     """
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index 1d7347f..495ed97 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -130,49 +130,49 @@ class TestQTLReaper(TestCase):
                     "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
-                       }]}]}])
+            {"T1": {"ID": "T1",
+                    "chromosomes": {
+                        1: {"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
+                                }]},
+                        2: {"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
+                                }]}}}})
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