From 2162cec2084f712993180618eb92c5a6dfdc5963 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 28 Dec 2023 13:19:50 +0300
Subject: Rework parsing of transposed geno files.

---
 tests/r_qtl/test_r_qtl2_geno.py | 125 +++++++++++++++++++++++-----------------
 1 file changed, 71 insertions(+), 54 deletions(-)

(limited to 'tests')

diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 908ef55..7b660a6 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -92,60 +92,77 @@ from r_qtl import r_qtl2 as rqtl2
              "EC.66C": 2
            })),
         ("tests/r_qtl/test_files/test_geno_transposed.zip",
-         ({"id": "1", "PVV4": 1},
-          {"id": "2", "PVV4": 1},
-          {"id": "3", "PVV4": 2},
-          {"id": "4", "PVV4": 1},
-          {"id": "5", "PVV4": 2},
-          {"id": "6", "PVV4": 2},
-          {"id": "7", "PVV4": 1},
-          {"id": "8", "PVV4": 2},
-          {"id": "9", "PVV4": None},
-          {"id": "10", "PVV4": 2},
-
-          {"id": "1", "AXR-1": 1},
-          {"id": "2", "AXR-1": 1},
-          {"id": "3", "AXR-1": 2},
-          {"id": "4", "AXR-1": 1},
-          {"id": "5", "AXR-1": 2},
-          {"id": "6", "AXR-1": 2},
-          {"id": "7", "AXR-1": 1},
-          {"id": "8", "AXR-1": 2},
-          {"id": "9", "AXR-1": 2},
-          {"id": "10", "AXR-1": 2},
-
-          {"id": "1", "HH.335C-Col/PhyA": 1},
-          {"id": "2", "HH.335C-Col/PhyA": 1},
-          {"id": "3", "HH.335C-Col/PhyA": None},
-          {"id": "4", "HH.335C-Col/PhyA": 1},
-          {"id": "5", "HH.335C-Col/PhyA": 2},
-          {"id": "6", "HH.335C-Col/PhyA": 2},
-          {"id": "7", "HH.335C-Col/PhyA": 1},
-          {"id": "8", "HH.335C-Col/PhyA": 2},
-          {"id": "9", "HH.335C-Col/PhyA": 2},
-          {"id": "10", "HH.335C-Col/PhyA": 2},
-
-          {"id": "1", "EC.480C": 1},
-          {"id": "2", "EC.480C": 1},
-          {"id": "3", "EC.480C": 1},
-          {"id": "4", "EC.480C": 1},
-          {"id": "5", "EC.480C": 2},
-          {"id": "6", "EC.480C": 2},
-          {"id": "7", "EC.480C": 1},
-          {"id": "8", "EC.480C": 1},
-          {"id": "9", "EC.480C": 2},
-          {"id": "10", "EC.480C": 2},
-
-          {"id": "1","EC.66C": 1},
-          {"id": "2", "EC.66C": 1},
-          {"id": "3", "EC.66C": 1},
-          {"id": "4", "EC.66C": 1},
-          {"id": "5", "EC.66C": 2},
-          {"id": "6", "EC.66C": 2},
-          {"id": "7", "EC.66C": 1},
-          {"id": "8", "EC.66C": 1},
-          {"id": "9", "EC.66C": 2},
-          {"id": "10", "EC.66C": 2}))))
+         ({
+             "id": "1",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+         }, {
+             "id": "2",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+         }, {
+             "id": "3",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": None,
+             "EC.480C": 1,
+             "EC.66C": 1
+         }, {
+             "id": "4",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+         },{
+             "id": "5",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+         }, {
+             "id": "6",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+         }, {
+             "id": "7",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+         }, {
+             "id": "8",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 1,
+             "EC.66C": 1
+         }, {
+             "id": "9",
+             "PVV4": None,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+         }, {
+             "id": "10",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+         }))))
 def test_parse_geno_files(relpath,expected):
     """
     GIVEN: Path to a zip file with R/qtl2 data
-- 
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