some unit test bugfixing

broadinstitute · Jan 9, 2024 · c800201 · c800201
1 parent 79a139f
commit c800201
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
@@ -470,11 +470,11 @@ def test_gapfill(self):
     def test_empty_fasta_input(self):
         inDir = util.file.get_test_input_path()
         empty_fasta = os.path.join(inDir, '..', 'empty.fasta')
-        with util.file.mkstempfname(suffix='.fasta') as out_fasta:
-            assembly.gapfill_gap2seq(in_scaffold=empty_fasta,
-                                     in_bam=os.path.join(inDir, 'G5012.3.testreads.bam'),
-                                     out_scaffold=out_fasta, random_seed=23923937, threads=1)
-            self.assertEqualContents(out_fasta, empty_fasta)
+        out_fasta = util.file.mkstempfname('.fasta')
+        assembly.gapfill_gap2seq(in_scaffold=empty_fasta,
+                                    in_bam=os.path.join(inDir, 'G5012.3.testreads.bam'),
+                                    out_scaffold=out_fasta, random_seed=23923937, threads=1)
+        self.assertEqualContents(out_fasta, empty_fasta)
 
 
 class TestImputeFromReference(TestCaseWithTmp):
@@ -568,7 +568,7 @@ def test_small_mummer(self):
             str(Bio.SeqIO.read(expected, 'fasta').seq))
 
     def test_empty_fasta_input(self):
-        inDir = util.file.get_test_input_path()
+        inDir = util.file.get_test_input_path(self)
         empty_fasta = os.path.join(inDir, '..', 'empty.fasta')
         outFasta = util.file.mkstempfname('.fasta')
         assembly.impute_from_reference(