From aaff8b8ac968bce9821d6fef22b1296247a9df09 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 24 Feb 2022 13:46:34 +0530 Subject: 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. --- gn3/computations/ctl.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn3/computations/ctl.py') 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) -- cgit v1.2.3