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| author | Arun Isaac | 2022-02-24 13:46:34 +0530 |
|---|---|---|
| committer | Arun Isaac | 2022-02-24 14:04:06 +0530 |
| commit | aaff8b8ac968bce9821d6fef22b1296247a9df09 (patch) | |
| tree | 87e7442b6f4114a64adeced052e3d3835b93a610 /tests/unit/computations | |
| parent | 393700a432e25336c5afd1f008152202853f5bc2 (diff) | |
| download | genenetwork3-aaff8b8ac968bce9821d6fef22b1296247a9df09.tar.gz | |
gn3: Explicitly specify UTF-8 to be the file encoding.
When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.
* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
*
tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 2 | ||||
| -rw-r--r-- | tests/unit/computations/test_wgcna.py | 2 |
2 files changed, 2 insertions, 2 deletions
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py index b36a93e..137c95c 100644 --- a/tests/unit/computations/test_gemma.py +++ b/tests/unit/computations/test_gemma.py @@ -22,7 +22,7 @@ class TestGemma(unittest.TestCase): self.assertEqual(_file, ("/tmp/gn2/phenotype_" "P7y6QWnwBPedSZdL0+m/GQ.txt")) open_mock.assert_called_with(("/tmp/gn2/phenotype_" - "P7y6QWnwBPedSZdL0+m/GQ.txt"), "w") + "P7y6QWnwBPedSZdL0+m/GQ.txt"), "w", encoding="utf-8") open_mock.return_value.write.assert_has_calls([ mock.call("NA\n"), mock.call("NA\n"), diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py index 3130374..a9108b0 100644 --- a/tests/unit/computations/test_wgcna.py +++ b/tests/unit/computations/test_wgcna.py @@ -166,7 +166,7 @@ class TestWgcna(TestCase): expected_input) file_handler.assert_called_once_with( - "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w') + "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w', encoding='utf-8') self.assertEqual( results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json") |