From c687f9460ca071c714cdc9cba62449b59b001de8 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 27 Dec 2023 12:12:33 +0300
Subject: Tests: Test parsing of non-transposed geno files.

Check that the parsing of non-transposed geno files.

Leave in failing test for transposed geno files.
---
 tests/r_qtl/test_r_qtl2_gmap.py | 48 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 tests/r_qtl/test_r_qtl2_gmap.py

(limited to 'tests/r_qtl/test_r_qtl2_gmap.py')

diff --git a/tests/r_qtl/test_r_qtl2_gmap.py b/tests/r_qtl/test_r_qtl2_gmap.py
new file mode 100644
index 0000000..64774c2
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_gmap.py
@@ -0,0 +1,48 @@
+"""Test the parsing of the R/qtl2 gmap files."""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "relpath,mapfiletype,expected",
+    (("tests/r_qtl/test_files/test_gmap.zip",
+      "genetic-map",
+      ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
+       {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
+       {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+       {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
+       {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
+     ("tests/r_qtl/test_files/test_gmap_transposed.zip",
+      "genetic-map",
+      ({"marker": "PVV4", "chr": "1", "pos": "0.000000"},
+       {"marker": "AXR-1", "chr": "1", "pos": "6.250674"},
+       {"marker": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+       {"marker": "EC.480C", "chr": "1", "pos": "12.577629"},
+       {"marker": "EC.66C", "chr": "1", "pos": "18.392830"})),
+     ("tests/r_qtl/test_files/test_pmap.zip",
+      "physical-map",
+      ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
+       {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
+       {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
+       {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"},
+       {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"})),
+     ("tests/r_qtl/test_files/test_pmap_transposed.zip",
+      "physical-map",
+      ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
+       {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
+       {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
+       {"marker": "D2Mit379", "chr": "2", "pos": "37.451062"},
+       {"marker": "D2Mit75", "chr": "2", "pos": "80.584782"}))))
+def test_parse_map_files(relpath, mapfiletype, expected):
+    """
+    GIVEN: A path to a zip file, `relpath` and the type of the map file,
+    WHEN: we parse the R/qtl2 map file,
+    THEN: ensure the parsed data is as expected.
+    """
+    with ZipFile(Path(relpath).absolute(), "r") as zfile:
+        assert rqtl2.map_data(
+            zfile, mapfiletype, rqtl2.control_data(zfile)) == expected
-- 
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