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| author | Alexander_Kabui | 2022-10-05 18:04:45 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2022-10-05 18:04:45 +0300 |
| commit | 4a8cf274dd72f13118d0f704f5e5e9fcf12dd202 (patch) | |
| tree | bcd2aa1f88367121a199d475a1d35d78056887bf | |
| parent | ff34aee0f39c2e91db243461d7d67405e7aea0e3 (diff) | |
| download | genenetwork3-bugfix/remove-pre-data-parsing.tar.gz | |
remove data preprocessing for tissue databugfix/remove-pre-data-parsing
| -rw-r--r-- | gn3/computations/rust_correlation.py | 8 |
1 files changed, 2 insertions, 6 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py index 8c3a0d3..5103de7 100644 --- a/gn3/computations/rust_correlation.py +++ b/gn3/computations/rust_correlation.py @@ -48,6 +48,7 @@ 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): @@ -67,7 +68,6 @@ 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 def __parse_line__(line): (trait_name, corr_coeff, p_val, num_overlap) = line.rstrip().split(",") if corr_type == "sample": @@ -155,12 +155,8 @@ def parse_tissue_corr_data(symbol_name: str, for (trait, symbol) in dataset_symbols.items(): try: corr_vals = dataset_vals.get(symbol.lower()) - if corr_vals: - corr_vals = [str(trait)] + corr_vals - - data.append(",".join([str(x) for x in corr_vals])) - + data.append([trait] + [str(val) for val in corr_vals]) except AttributeError: pass |