From 9eab14f7f6c40c401c29d11d69ac54303415ab87 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 4 Jan 2024 11:50:04 +0300
Subject: Process sex and cross information data in "covar" files.

---
 tests/r_qtl/test_files/test_covar.zip            | Bin 490 -> 562 bytes
 tests/r_qtl/test_files/test_covar_transposed.zip | Bin 541 -> 594 bytes
 tests/r_qtl/test_r_qtl2_covar.py                 |  30 +++++++++++++----------
 3 files changed, 17 insertions(+), 13 deletions(-)

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/test_covar.zip b/tests/r_qtl/test_files/test_covar.zip
index 6fbb5e9..61961a0 100644
Binary files a/tests/r_qtl/test_files/test_covar.zip and b/tests/r_qtl/test_files/test_covar.zip differ
diff --git a/tests/r_qtl/test_files/test_covar_transposed.zip b/tests/r_qtl/test_files/test_covar_transposed.zip
index 5e933cc..c0758a3 100644
Binary files a/tests/r_qtl/test_files/test_covar_transposed.zip and b/tests/r_qtl/test_files/test_covar_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_covar.py b/tests/r_qtl/test_r_qtl2_covar.py
index c18ee74..eef7a33 100644
--- a/tests/r_qtl/test_r_qtl2_covar.py
+++ b/tests/r_qtl/test_r_qtl2_covar.py
@@ -10,19 +10,21 @@ from r_qtl import r_qtl2 as rqtl2
 @pytest.mark.parametrize(
     "filepath,expected",
     (("tests/r_qtl/test_files/test_covar.zip",
-      ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})),
+      ({"id": "1", "sex": "male", "cross_direction": 1},
+       {"id": "2", "sex": "male", "cross_direction": 1},
+       {"id": "3", "sex": "male", "cross_direction": 1},
+       {"id": "71", "sex": "male", "cross_direction": 0},
+       {"id": "72", "sex": "male", "cross_direction": 0},
+       {"id": "146", "sex": "female", "cross_direction": 1},
+       {"id": "147", "sex": "female", "cross_direction": 1},
+       {"id": "148", "sex": "female", "cross_direction": 1})),
      ("tests/r_qtl/test_files/test_covar_transposed.zip",
-      ({"id": "1", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "2", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "3", "sex": "m", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "146", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "147", "sex": "f", "cross_direction": "(BxS)x(BxS)"},
-       {"id": "148", "sex": "f", "cross_direction": "(BxS)x(BxS)"})),
+      ({"id": "1", "sex": "male", "cross_direction": 1},
+       {"id": "2", "sex": "male", "cross_direction": 1},
+       {"id": "3", "sex": "male", "cross_direction": 1},
+       {"id": "146", "sex": "female", "cross_direction": 1},
+       {"id": "147", "sex": "female", "cross_direction": 1},
+       {"id": "148", "sex": "female", "cross_direction": 1})),
      ))
 def test_parse_covar_files(filepath, expected):
     """Test parsing of 'covar' files from the R/qtl2 bundle.
@@ -33,4 +35,6 @@ def test_parse_covar_files(filepath, expected):
     """
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
         cdata = rqtl2.control_data(zfile)
-        assert tuple(rqtl2.file_data(zfile, "covar", cdata)) == expected
+        process_fns = rqtl2.make_process_data_covar(cdata)
+        assert tuple(
+            rqtl2.file_data(zfile, "covar", cdata, *process_fns)) == expected
-- 
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