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authorFrederick Muriuki Muriithi2024-01-10 04:44:53 +0300
committerFrederick Muriuki Muriithi2024-01-10 04:44:53 +0300
commit9322da0f79dfa4c3f9f899f5a861ce302ce21e9c (patch)
treead3ac4b8d5791219392eba77067c2c0ce71e25e1 /tests/r_qtl
parent21078fecb698972062af3157a9a0f6e84bb8fd0d (diff)
downloadgn-uploader-9322da0f79dfa4c3f9f899f5a861ce302ce21e9c.tar.gz
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.
Diffstat (limited to 'tests/r_qtl')
-rw-r--r--tests/r_qtl/test_r_qtl2_map_files.py40
-rw-r--r--tests/r_qtl/test_r_qtl2_pheno.py20
2 files changed, 30 insertions, 30 deletions
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.