diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 15 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 16 |
2 files changed, 17 insertions, 14 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 3633a59..f7ddfd0 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -141,7 +141,7 @@ def find_identical_traits( return acc + ident[1] def __dictify_controls__(acc, control_item): - ckey = tuple("{:.3f}".format(item) for item in control_item[0]) + ckey = tuple("{item:.3f}" for item in control_item[0]) return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)} return (reduce(## for identical control traits @@ -181,8 +181,8 @@ def tissue_correlation( assert len(primary_trait_values) == len(target_trait_values), ( "The lengths of the `primary_trait_values` and `target_trait_values` " "must be equal") - assert method in method_fns.keys(), ( - "Method must be one of: {}".format(",".join(method_fns.keys()))) + assert method in method_fns, ( + "Method must be one of: {','.join(method_fns.keys())}") corr, pvalue = method_fns[method](primary_trait_values, target_trait_values) return (corr, pvalue) @@ -241,7 +241,7 @@ def partial_correlations_fast(# pylint: disable=[R0913, R0914] function in GeneNetwork1. """ assert method in ("spearman", "pearson") - with open(database_filename, "r") as dataset_file: + with open(database_filename, "r") as dataset_file: # pytest: disable=[W1514] dataset = tuple(dataset_file.readlines()) good_dataset_samples = good_dataset_samples_indexes( @@ -290,12 +290,15 @@ def build_data_frame( if isinstance(zdata[0], float): return x_y_df.join(pandas.DataFrame({"z": zdata})) interm_df = x_y_df.join(pandas.DataFrame( - {"z{}".format(i): val for i, val in enumerate(zdata)})) + {f"z{i}": val for i, val in enumerate(zdata)})) if interm_df.shape[1] == 3: return interm_df.rename(columns={"z0": "z"}) return interm_df def compute_trait_info(primary_vals, control_vals, target, method): + """ + Compute the correlation values for the given arguments. + """ targ_vals = target[0] targ_name = target[1] primary = [ @@ -629,7 +632,7 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911] "status": "not-found", "message": "None of the requested control traits were found."} for trait in cntrl_traits: - if trait["haveinfo"] == False: + if trait["haveinfo"] is False: warnings.warn( (f"Control traits {trait['trait_fullname']} was not found " "- continuing without it."), 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] |