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/parsers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn3/computations/parsers.py')

diff --git a/gn3/computations/parsers.py b/gn3/computations/parsers.py
index 1af35d6..79e3955 100644
--- a/gn3/computations/parsers.py
+++ b/gn3/computations/parsers.py
@@ -15,7 +15,7 @@ def parse_genofile(file_path: str) -> Tuple[List[str],
         'u': None,
     }
     genotypes, samples = [], []
-    with open(file_path, "r") as _genofile:
+    with open(file_path, "r", encoding="utf-8") as _genofile:
         for line in _genofile:
             line = line.strip()
             if line.startswith(("#", "@")):
-- 
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