diff options
| -rw-r--r-- | gn3/computations/rust_correlation.py | 42 |
1 files changed, 23 insertions, 19 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index 9f991b2..d206065 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -57,7 +57,7 @@ def generate_json_file(tmp_dir, tmp_file, def run_correlation(dataset, trait_vals: - list[str], + str, method: str, delimiter: str): """entry function to call rust correlation""" @@ -84,6 +84,10 @@ def parse_correlation_output(result_file: str, top_n: int = 500) -> list[dict]: corr_results = [] + breakpoint() + + + with open(result_file, "r", encoding="utf-8") as file_reader: lines = [next(file_reader) for x in range(top_n)] @@ -120,7 +124,7 @@ def get_samples(all_samples: dict[str, str], return data - return({key: float(val) for (key, val) in all_samples.items() + return({key: float(val.strip()) for (key, val) in all_samples.items() if key not in excluded and val.lower().strip() != "x"}) @@ -145,26 +149,26 @@ def get_sample_corr_data(sample_type: str, return data -def parse_tissue_corr_data(tt_symbol: list[dict[str, str]], - symbols_dict: [str, str], - dataset_dict): - """get the correct datatype""" +def parse_tissue_corr_data(symbol_name: str, + symbol_dict: dict[list[str, list[str]]], + dataset_symbols: dict[str, str], + dataset_vals: dict[str, list[str, str]]): + + if symbol_name and symbol_name.lower() in symbol_dict: + x_vals = ",".join([str(val) + for val in symbol_dict[symbol_name.lower()]]) - data = [] + data = [] - if not (tt_symbol): - return [[], []] + for (trait, symbol) in dataset_symbols.items(): + try: + corr_vals = dataset_vals.get(symbol.lower()) - for (name, symbol) in symbols_dict.items(): - try: - exists = dataset_dict.get(symbol.lower()) - if exists: - corr_values = insert(0, name) - ",".join([str(dt) for dt in data]) + corr_vals.insert(0, trait) - data.append(corr_values) + data.append(",".join([str(val) for val in corr_vals])) - except Exception as e: - pass + except Exception as e: + pass - return [symbol[0], data] + return (x_vals, data) |