From 3294adc11ada56046ff748c08b97faf0eeed11b2 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 27 Dec 2023 08:26:27 +0300
Subject: Tests: Test parsing of pmap files. Merge testing of map files.

---
 tests/r_qtl/test_files/test_pmap.zip            | Bin 0 -> 531 bytes
 tests/r_qtl/test_files/test_pmap_transposed.zip | Bin 0 -> 583 bytes
 tests/r_qtl/test_r_qtl2.py                      |  43 ++++++++++++------------
 3 files changed, 22 insertions(+), 21 deletions(-)
 create mode 100644 tests/r_qtl/test_files/test_pmap.zip
 create mode 100644 tests/r_qtl/test_files/test_pmap_transposed.zip

diff --git a/tests/r_qtl/test_files/test_pmap.zip b/tests/r_qtl/test_files/test_pmap.zip
new file mode 100644
index 0000000..a3fadd5
Binary files /dev/null and b/tests/r_qtl/test_files/test_pmap.zip differ
diff --git a/tests/r_qtl/test_files/test_pmap_transposed.zip b/tests/r_qtl/test_files/test_pmap_transposed.zip
new file mode 100644
index 0000000..5d9f51b
Binary files /dev/null and b/tests/r_qtl/test_files/test_pmap_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2.py b/tests/r_qtl/test_r_qtl2.py
index a72b300..33ff5e5 100644
--- a/tests/r_qtl/test_r_qtl2.py
+++ b/tests/r_qtl/test_r_qtl2.py
@@ -8,40 +8,41 @@ from r_qtl import r_qtl2 as rqtl2
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
-    "relpath,expected",
+    "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"}))))
-def test_parse_gmap_files(relpath, expected):
+       {"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`
-    WHEN: we parse a gmap file
+    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, "genetic-map", rqtl2.control_data(zfile)) == expected
-
-@pytest.mark.skip(reason="Test not implemented yet.")
-@pytest.mark.unit_test
-@pytest.mark.parametrize(
-    "relpath,expected",
-    (("tests/r_qtl/test_files/test_pmap.zip",
-      ()),
-     ("tests/r_qtl/test_files/test_pmap_transposed.zip",
-      ())))
-def test_parse_pmap_files(relpath, expected):
-    """
-    GIVEN: A path to a zip file, `relpath`
-    WHEN: we parse a pmap file
-    THEN: ensure the parsed data is as expected.
-    """
+            zfile, mapfiletype, rqtl2.control_data(zfile)) == expected
-- 
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