From d4fff5fda2d9fe2b9730a7cffcc8f85b3a8eff17 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 28 Dec 2023 09:55:26 +0300
Subject: Handle transposed geno files.

---
 tests/r_qtl/test_r_qtl2_geno.py | 134 ++++++++++++++++------------------------
 1 file changed, 54 insertions(+), 80 deletions(-)

(limited to 'tests/r_qtl')

diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 5ebb5a9..908ef55 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -92,86 +92,60 @@ from r_qtl import r_qtl2 as rqtl2
              "EC.66C": 2
            })),
         ("tests/r_qtl/test_files/test_geno_transposed.zip",
-         ({
-             "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
-           }))))
+         ({"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}))))
 def test_parse_geno_files(relpath,expected):
     """
     GIVEN: Path to a zip file with R/qtl2 data
-- 
cgit v1.2.3