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_geno.py  |  8 ++++++--
 tests/r_qtl/test_r_qtl2_gmap.py  | 12 ++++++------
 tests/r_qtl/test_r_qtl2_pheno.py |  4 ++--
 3 files changed, 14 insertions(+), 10 deletions(-)

(limited to 'tests/r_qtl')

diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index 787d13a..c33984e 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -171,8 +171,12 @@ def test_parse_geno_files(relpath, expected):
     THEN: ensure that the data we get is as expected
     """
     with ZipFile(Path(relpath).absolute(), "r") as zfile:
-        assert tuple(
-            rqtl2.genotype_data(zfile, rqtl2.control_data(zfile))) == expected
+        cdata = rqtl2.control_data(zfile)
+        assert tuple(rqtl2.file_data(
+            zfile,
+            "geno",
+            cdata,
+            *rqtl2.make_process_data_geno(cdata))) == expected
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
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
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index 554d9c8..46be469 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -29,5 +29,5 @@ def test_parse_pheno_files(filepath, expected):
     THEN: verify the parsed data is as expected
     """
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
-        assert tuple(
-            rqtl2.phenotype_data(zfile, rqtl2.control_data(zfile))) == expected
+        cdata = rqtl2.control_data(zfile)
+        assert tuple(rqtl2.file_data(zfile, "pheno", cdata)) == expected
-- 
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