From 46410163ca402660434b09a8fc8ec7b12b89d8a1 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 27 Dec 2023 08:08:31 +0300
Subject: Tests: Add tests for parsing gmap files.

---
 tests/r_qtl/test_files/test_gmap.zip            | Bin 0 -> 542 bytes
 tests/r_qtl/test_files/test_gmap_transposed.zip | Bin 0 -> 594 bytes
 tests/r_qtl/test_r_qtl2.py                      |  47 ++++++++++++++++++++++++
 3 files changed, 47 insertions(+)
 create mode 100644 tests/r_qtl/test_files/test_gmap.zip
 create mode 100644 tests/r_qtl/test_files/test_gmap_transposed.zip
 create mode 100644 tests/r_qtl/test_r_qtl2.py

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/test_gmap.zip b/tests/r_qtl/test_files/test_gmap.zip
new file mode 100644
index 0000000..c8d452a
Binary files /dev/null and b/tests/r_qtl/test_files/test_gmap.zip differ
diff --git a/tests/r_qtl/test_files/test_gmap_transposed.zip b/tests/r_qtl/test_files/test_gmap_transposed.zip
new file mode 100644
index 0000000..74a956e
Binary files /dev/null and b/tests/r_qtl/test_files/test_gmap_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2.py b/tests/r_qtl/test_r_qtl2.py
new file mode 100644
index 0000000..a72b300
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2.py
@@ -0,0 +1,47 @@
+"""Test the parsing of the R/qtl2 data 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,expected",
+    (("tests/r_qtl/test_files/test_gmap.zip",
+      ({"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",
+      ({"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):
+    """
+    GIVEN: A path to a zip file, `relpath`
+    WHEN: we parse a gmap 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.
+    """
-- 
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