From 9322da0f79dfa4c3f9f899f5a861ce302ce21e9c Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 10 Jan 2024 04:44:53 +0300
Subject: Make identifier column name explicit

Since the R/qtl2 bundle generator could name the identifier column
anything, this commit converts the incoming identifier column name
into something explicit that we know and can use.
---
 tests/r_qtl/test_r_qtl2_map_files.py | 40 ++++++++++++++++++------------------
 tests/r_qtl/test_r_qtl2_pheno.py     | 20 +++++++++---------
 2 files changed, 30 insertions(+), 30 deletions(-)

(limited to 'tests')

diff --git a/tests/r_qtl/test_r_qtl2_map_files.py b/tests/r_qtl/test_r_qtl2_map_files.py
index 5c8ca6a..3427ffb 100644
--- a/tests/r_qtl/test_r_qtl2_map_files.py
+++ b/tests/r_qtl/test_r_qtl2_map_files.py
@@ -11,32 +11,32 @@ from r_qtl import r_qtl2 as rqtl2
     "relpath,mapfiletype,expected",
     (("tests/r_qtl/test_files/test_gmap.zip",
       "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"})),
+      ({"id": "PVV4", "chr": "1", "pos": "0.000000"},
+       {"id": "AXR-1", "chr": "1", "pos": "6.250674"},
+       {"id": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+       {"id": "EC.480C", "chr": "1", "pos": "12.577629"},
+       {"id": "EC.66C", "chr": "1", "pos": "18.392830"})),
      ("tests/r_qtl/test_files/test_gmap_transposed.zip",
       "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"})),
+      ({"id": "PVV4", "chr": "1", "pos": "0.000000"},
+       {"id": "AXR-1", "chr": "1", "pos": "6.250674"},
+       {"id": "HH.335C-Col/PhyA", "chr": "1", "pos": "9.303868"},
+       {"id": "EC.480C", "chr": "1", "pos": "12.577629"},
+       {"id": "EC.66C", "chr": "1", "pos": "18.392830"})),
      ("tests/r_qtl/test_files/test_pmap.zip",
       "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"})),
+      ({"id": "D1Mit18", "chr": "1", "pos": "52.418656"},
+       {"id": "D1Mit80", "chr": "1", "pos": "86.377953"},
+       {"id": "D1Mit17", "chr": "1", "pos": "189.571337"},
+       {"id": "D2Mit379", "chr": "2", "pos": "37.451062"},
+       {"id": "D2Mit75", "chr": "2", "pos": "80.584782"})),
      ("tests/r_qtl/test_files/test_pmap_transposed.zip",
       "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"}))))
+      ({"id": "D1Mit18", "chr": "1", "pos": "52.418656"},
+       {"id": "D1Mit80", "chr": "1", "pos": "86.377953"},
+       {"id": "D1Mit17", "chr": "1", "pos": "189.571337"},
+       {"id": "D2Mit379", "chr": "2", "pos": "37.451062"},
+       {"id": "D2Mit75", "chr": "2", "pos": "80.584782"}))))
 def test_parse_map_files(relpath, mapfiletype, expected):
     """
     GIVEN: A path to a zip file, `relpath` and the type of the map file,
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index 66850a0..a7de675 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -36,17 +36,17 @@ def test_parse_pheno_files(filepath, expected):
 @pytest.mark.parametrize(
     "filepath,expected",
     (("tests/r_qtl/test_files/test_phenocovar.zip",
-      ({"pheno": "T0", "time (hrs)": "0"},
-       {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
-       {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
-       {"pheno": "T6", "time (hrs)": "0.1"},
-       {"pheno": "T8", "time (hrs)": "0.133333333333333"})),
+      ({"id": "T0", "time (hrs)": "0"},
+       {"id": "T2", "time (hrs)": "0.0333333333333333"},
+       {"id": "T4", "time (hrs)": "0.0666666666666667"},
+       {"id": "T6", "time (hrs)": "0.1"},
+       {"id": "T8", "time (hrs)": "0.133333333333333"})),
      ("tests/r_qtl/test_files/test_phenocovar_transposed.zip",
-      ({"pheno": "T0", "time (hrs)": "0"},
-       {"pheno": "T2", "time (hrs)": "0.0333333333333333"},
-       {"pheno": "T4", "time (hrs)": "0.0666666666666667"},
-       {"pheno": "T6", "time (hrs)": "0.1"},
-       {"pheno": "T8", "time (hrs)": "0.133333333333333"}))))
+      ({"id": "T0", "time (hrs)": "0"},
+       {"id": "T2", "time (hrs)": "0.0333333333333333"},
+       {"id": "T4", "time (hrs)": "0.0666666666666667"},
+       {"id": "T6", "time (hrs)": "0.1"},
+       {"id": "T8", "time (hrs)": "0.133333333333333"}))))
 def test_parse_phenocovar_files(filepath, expected):
     """Test parsing of 'phenocovar' files from the R/qtl2 bundle.
 
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