From 3e51fb24fd34bab2164a5f4056bc78d21827ca29 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 3 Jan 2024 16:53:40 +0300
Subject: Use generic parser. Remove obsoleted functions.

---
 tests/r_qtl/test_r_qtl2_gmap.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(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
index ba46c42..5c8ca6a 100644
--- a/tests/r_qtl/test_r_qtl2_gmap.py
+++ b/tests/r_qtl/test_r_qtl2_gmap.py
@@ -10,28 +10,28 @@ from r_qtl import r_qtl2 as rqtl2
 @pytest.mark.parametrize(
     "relpath,mapfiletype,expected",
     (("tests/r_qtl/test_files/test_gmap.zip",
-      "genetic-map",
+      "gmap",
       ({"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",
+      "gmap",
       ({"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",
+      "pmap",
       ({"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",
+      "pmap",
       ({"marker": "D1Mit18", "chr": "1", "pos": "52.418656"},
        {"marker": "D1Mit80", "chr": "1", "pos": "86.377953"},
        {"marker": "D1Mit17", "chr": "1", "pos": "189.571337"},
@@ -44,5 +44,5 @@ def test_parse_map_files(relpath, mapfiletype, expected):
     THEN: ensure the parsed data is as expected.
     """
     with ZipFile(Path(relpath).absolute(), "r") as zfile:
-        assert tuple(rqtl2.map_data(
-            zfile, mapfiletype, rqtl2.control_data(zfile))) == expected
+        cdata = rqtl2.control_data(zfile)
+        assert tuple(rqtl2.file_data(zfile, mapfiletype, cdata)) == expected
-- 
cgit v1.2.3