diff options
Diffstat (limited to 'gn3/computations/qtlreaper.py')
| -rw-r--r-- | gn3/computations/qtlreaper.py | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index d1ff4ac..b61bdae 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -27,7 +27,7 @@ def generate_traits_file(samples, trait_values, traits_filename): ["{}\t{}".format( len(trait_values), "\t".join([str(i) for i in t])) for t in trait_values[-1:]]) - with open(traits_filename, "w") as outfile: + with open(traits_filename, "w", encoding="utf8") as outfile: outfile.writelines(data) def create_output_directory(path: str): @@ -68,13 +68,13 @@ def run_reaper( The function will raise a `subprocess.CalledProcessError` exception in case of any errors running the `qtlreaper` command. """ - create_output_directory("{}/qtlreaper".format(output_dir)) - output_filename = "{}/qtlreaper/main_output_{}.txt".format( - output_dir, random_string(10)) + create_output_directory(f"{output_dir}/qtlreaper") + output_filename = ( + f"{output_dir}/qtlreaper/main_output_{random_string(10)}.txt") output_list = ["--main_output", output_filename] if separate_nperm_output: - permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format( - output_dir, random_string(10)) + permu_output_filename: Union[None, str] = ( + f"{output_dir}/qtlreaper/permu_output_{random_string(10)}.txt") output_list = output_list + [ "--permu_output", permu_output_filename] # type: ignore[list-item] else: @@ -135,7 +135,7 @@ def parse_reaper_main_results(results_file): """ Parse the results file of running QTLReaper into a list of dicts. """ - with open(results_file, "r") as infile: + with open(results_file, "r", encoding="utf8") as infile: lines = infile.readlines() def __parse_column_float_value(value): @@ -164,7 +164,7 @@ def parse_reaper_permutation_results(results_file): """ Parse the results QTLReaper permutations into a list of values. """ - with open(results_file, "r") as infile: + with open(results_file, "r", encoding="utf8") as infile: lines = infile.readlines() return [float(line.strip()) for line in lines] |