diff options
| -rw-r--r-- | gn3/computations/rust_correlation.py | 66 |
1 files changed, 19 insertions, 47 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index 57c1b12..831ef35 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -69,11 +69,11 @@ def run_correlation(dataset, trait_vals: command_list = [CORRELATION_COMMAND, json_file, TMPDIR] - rls = subprocess.run(command_list, check=True) + subprocess.run(command_list, check=True) - rs = parse_correlation_output(output_file,10000) + results = parse_correlation_output(output_file, 500) - return rs + return results def parse_correlation_output(result_file: str, top_n: int = 500) -> list[dict]: @@ -99,51 +99,23 @@ def parse_correlation_output(result_file: str, top_n: int = 500) -> list[dict]: return corr_results +def get_samples(all_samples: dict[str, str], + base_samples: list[str], + excluded: list[str]): + """filter null samples and excluded samples""" + data = {} -# computation specific;sample_r,lit_corr -def compute_top_n(first_run_results,init_type,dataset_1,dataset_2,dataset_type:str): - if dataset__type.lower()!= "probeset": - return first_run_results - - if init_type == "sample": - # do both lit and tissue - - results_a = run_correlation(dataset_1, x_vals_1,method,delimiter) - - results_b = lit_correlation_for_trait(unkown) - - - # question how do we merge this - - - - - - if init_type == "tissue": - # do sample and tissue - - - file_a = run_correlation(dataset_1,x_vals_1,method,delimiter) - - result_b = lit_correlation_for_trait(unkown) - - # merge the results - - - - if init_type == "lit": - - file_a = run_correlation() - - file_b = run_correlation() - - join <(file_a) <(file_b) - - # do the merge here - # do both sample and tissue - - - + if base_samples: + fls = [ + sm for sm in base_samples if sm not in excluded] + for sample in fls: + if sample in all_samples: + smp_val = all_samples[sample].strip() + if smp_val.lower() != "x": + data[sample] = float(smp_val) + return data + return({key: float(val) for (key, val) in all_samples.items() + if key not in excluded and val.lower().strip() != "x"}) |