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.

1 files changed, 2 insertions, 2 deletions

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 0433b3f..b3539a9 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -56,7 +56,7 @@ def process_rqtl_output(file_name: str) -> List:
     # Later I should probably redo this using csv.read to avoid the
     # awkwardness with removing quotes with [1:-1]
     with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
-                           "output", file_name), "r") as the_file:
+                           "output", file_name), "r", encoding="utf-8") as the_file:
         for line in the_file:
             line_items = line.split(",")
             if line_items[1][1:-1] == "chr" or not line_items:
@@ -88,7 +88,7 @@ def process_perm_output(file_name: str):
     """
     perm_results = []
     with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
-                           "output", "PERM_" + file_name), "r") as the_file:
+                           "output", "PERM_" + file_name), "r", encoding="utf-8") as the_file:
         for i, line in enumerate(the_file):
             if i == 0:
                 # Skip header line