diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/rust_correlation.py | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index dde6188..644c73b 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -48,12 +48,13 @@ def generate_json_file( return (output_file, tmp_json_file) + def run_correlation( dataset, trait_vals: str, method: str, delimiter: str, corr_type: str = "sample", top_n: int = 500): """entry function to call rust correlation""" - #pylint: disable=too-many-arguments + # pylint: disable=too-many-arguments (tmp_dir, tmp_file) = generate_input_files(dataset) (output_file, json_file) = generate_json_file( tmp_dir=tmp_dir, tmp_file=tmp_file, method=method, delimiter=delimiter, @@ -74,7 +75,7 @@ def run_correlation( def parse_correlation_output(result_file: str, corr_type: str, top_n: int = 500) -> dict: """parse file output """ - #current types are sample and tissue + # current types are sample and tissue def __parse_line__(line): (trait_name, corr_coeff, p_val, num_overlap) = line.rstrip().split(",") if corr_type == "sample": @@ -126,23 +127,24 @@ def get_samples(all_samples: dict[str, str], def get_sample_corr_data(sample_type: str, - all_samples: dict[str, str], + sample_data: dict[str, str], + all_samples: list[str], dataset_samples: list[str]) -> dict[str, str]: """dependeing on the sample_type fetch the correct sample data """ if sample_type == "samples_primary": - data = get_samples(all_samples=all_samples, + data = get_samples(all_samples=sample_data, base_samples=dataset_samples, excluded=[]) elif sample_type == "samples_other": data = get_samples( - all_samples=all_samples, + all_samples=sample_data, base_samples=[], excluded=dataset_samples) else: data = get_samples( - all_samples=all_samples, base_samples=[], excluded=[]) + all_samples=sample_data, base_samples=all_samples, excluded=[]) return data |