diff options
Diffstat (limited to 'gn3/computations/partial_correlations.py')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 15 |
1 files changed, 9 insertions, 6 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."), |