Minor refactorization

sgkit-dev · Sep 20, 2024 · aff19f2 · aff19f2
1 parent f94234e
commit aff19f2
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/bio2zarr/bed2zarr.py b/bio2zarr/bed2zarr.py
@@ -325,6 +325,12 @@ def make_field_def(name, alias, dtype=None, *, description=""):
     return fields[:num_fields]
 
 
+def mkfields(bed_type):
+    mandatory = mandatory_bed_field_definitions()
+    optional = optional_bed_field_definitions(bed_type.value - BedType.BED3.value)
+    return mandatory + optional
+
+
 def mkschema(bed_path, out):
     bed_type = guess_bed_file_type(bed_path)
     data = pd.read_table(bed_path, header=None)
@@ -335,12 +341,6 @@ def mkschema(bed_path, out):
     out.write(spec.asjson())
 
 
-def mkfields(bed_type):
-    mandatory = mandatory_bed_field_definitions()
-    optional = optional_bed_field_definitions(bed_type.value - BedType.BED3.value)
-    return mandatory + optional
-
-
 def bed2zarr_init(
     bed_path,
     bed_type,

diff --git a/tests/test_bed.py b/tests/test_bed.py
@@ -93,7 +93,7 @@ class TestBedData:
     @pytest.mark.parametrize("bed_data", ALL_BED_FORMATS, indirect=True)
     def test_guess_bed_type_from_path(self, bed_path, request):
         bedspec = request.node.callspec.params["bed_data"]
-        if bedspec in [2, 10, 11, 13]:
+        if bedspec in DISALLOWED_BED_FORMATS:
             with pytest.raises(ValueError):
                 bed2zarr.guess_bed_file_type(bed_path)
         else: