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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 /gn3/computations/ctl.py | |
| 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 'gn3/computations/ctl.py')
| -rw-r--r-- | gn3/computations/ctl.py | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py index 238740f..f881410 100644 --- a/gn3/computations/ctl.py +++ b/gn3/computations/ctl.py @@ -16,7 +16,7 @@ def call_ctl_script(data): cmd = compose_wgcna_cmd("ctl_analysis.R", temp_file_name) cmd_results = run_cmd(cmd) - with open(temp_file_name, "r") as outputfile: + with open(temp_file_name, "r", encoding="utf-8") as outputfile: if cmd_results["code"] != 0: return (cmd_results, None) output_file_data = json.load(outputfile) |