aboutsummaryrefslogtreecommitdiff
path: root/tests/r_qtl
diff options
context:
space:
mode:
Diffstat (limited to 'tests/r_qtl')
-rw-r--r--tests/r_qtl/test_r_qtl2_qc.py19
1 files changed, 12 insertions, 7 deletions
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index d12172e..05db30e 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -124,9 +124,12 @@ def test_missing_files(filepath, expected):
("tests/r_qtl/test_files/test_geno.zip",
tuple()),
("tests/r_qtl/test_files/geno_with_missing_genotypes.zip",
- (InvalidValue(1, "AXR-1", "X", "Invalid value 'X'. Expected one of ('L', 'C')."),
- InvalidValue(2, "EC.480C", "Y", "Invalid value 'Y'. Expected one of ('L', 'C')."),
- InvalidValue(6, "HH.335C-Col/PhyA", "H", f"Invalid value 'H'. Expected one of ('L', 'C').")))))
+ (InvalidValue("geno", 1, "AXR-1", "X",
+ "Invalid value 'X'. Expected one of ('L', 'C')."),
+ InvalidValue("geno", 2, "EC.480C",
+ "Y", "Invalid value 'Y'. Expected one of ('L', 'C')."),
+ InvalidValue("geno", 6, "HH.335C-Col/PhyA", "H",
+ f"Invalid value 'H'. Expected one of ('L', 'C').")))))
def test_geno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle
@@ -145,10 +148,12 @@ def test_geno_errors(filepath, expected):
("tests/r_qtl/test_files/pheno_without_errors.zip",
tuple()),
("tests/r_qtl/test_files/pheno_with_errors.zip",
- (InvalidValue(1, "liver", "61.92", ("Invalid value '61.92'. Expected numerical value "
- "with at least 3 decimal places.")),
- InvalidValue(2, "spleen", "brrr", ("Invalid value 'brrr'. Expected numerical value "
- "with at least 3 decimal places."))))))
+ (InvalidValue("pheno", 1, "liver", "61.92", (
+ "Invalid value '61.92'. Expected numerical value "
+ "with at least 3 decimal places.")),
+ InvalidValue("pheno", 2, "spleen", "brrr", (
+ "Invalid value 'brrr'. Expected numerical value "
+ "with at least 3 decimal places."))))))
def test_pheno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle