fix(generate): ped parser accept None value as null

natir · May 9, 2023 · 67bf3fd · 67bf3fd
1 parent a7c45fc
commit 67bf3fd
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Showing 2 changed files with 3 additions and 6 deletions.
diff --git a/src/variantplaner/io/ped.py b/src/variantplaner/io/ped.py
@@ -27,6 +27,7 @@ def into_lazyframe(input_path: pathlib.Path) -> polars.LazyFrame:
         input_path,
         separator="\t",
         has_header=False,
+        null_values="None",
         new_columns=["family_id", "personal_id", "father_id", "mother_id", "sex", "affected"],
         dtypes={
             "family_id": polars.Utf8,

diff --git a/tests/test_generate.py b/tests/test_generate.py
@@ -31,10 +31,8 @@ def test_transmission(tmp_path: pathlib.Path) -> None:
     filecmp.cmp(truth, out_path)
 
 
-def test_transmission_missing_mother(tmp_path: pathlib.Path) -> None:
+def test_transmission_missing_mother() -> None:
     """Check add_origin of genotype."""
-    out_path = tmp_path / "transmission.parquet"
-
     genotypes_lf = polars.scan_parquet(DATA_DIR / "no_info.genotypes.parquet")
     genotypes_lf = genotypes_lf.filter(polars.col("sample") != "sample_3")
 
@@ -50,10 +48,8 @@ def test_transmission_missing_mother(tmp_path: pathlib.Path) -> None:
     assert transmission.get_column("mother_gq").to_list() == [None, None, None, None, None]
 
 
-def test_transmission_missing_father(tmp_path: pathlib.Path) -> None:
+def test_transmission_missing_father() -> None:
     """Check add_origin of genotype."""
-    out_path = tmp_path / "transmission.parquet"
-
     genotypes_lf = polars.scan_parquet(DATA_DIR / "no_info.genotypes.parquet")
     genotypes_lf = genotypes_lf.filter(polars.col("sample") != "sample_2")