From 679a1af832ad9585c7cf72996043edb08e1b0d10 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 6 Sep 2021 08:06:14 +0300
Subject: Leave "Chr" value as string when parsing

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

* The "Chr" value seems to be mostly a name of some sort, despite it being,
  seemingly an number. This commit parses the "Chr" value as a string.
  It also updates the tests to expec a string, rather than a number for "Chr"
  values.
---
 gn3/computations/qtlreaper.py             |  5 +++--
 tests/unit/computations/test_qtlreaper.py | 20 ++++++++++----------
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index eff2a80..9b20309 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -94,7 +94,7 @@ def parse_reaper_main_results(results_file):
     with open(results_file, "r") as infile:
         lines = infile.readlines()
 
-    def __parse_column_value(value):
+    def __parse_column_float_value(value):
         try:
             return float(value)
         except:
@@ -102,7 +102,8 @@ def parse_reaper_main_results(results_file):
 
     def __parse_line(line):
         items = line.strip().split("\t")
-        return items[0:2] + [__parse_column_value(item) for item in items[2:]]
+        return items[0:3] + [
+            __parse_column_float_value(item) for item in items[3:]]
 
     header = lines[0].strip().split("\t")
     return [dict(zip(header, __parse_line(line))) for line in lines[1:]]
diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
index 6c3b64d..fd3434a 100644
--- a/tests/unit/computations/test_qtlreaper.py
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -13,52 +13,52 @@ class TestQTLReaper(TestCase):
                 "tests/unit/computations/data/qtlreaper/main_output_sample.txt"),
             [
                 {
-                    "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "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,
+                    "ID": "T1", "Locus": "rs36742481", "Chr": "1", "cM": 2.140,
                     "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
                     "pValue": 1.000
                 }
-- 
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