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| author | Frederick Muriuki Muriithi | 2022-07-28 10:21:58 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-07-28 10:21:58 +0300 |
| commit | 82922e5a052abf22b9d458ddebaf8ee523bd6f55 (patch) | |
| tree | 74f4fdbce3d579f71b816d9d222f4c1e95383c4e | |
| parent | a08d91a234f700043d1d31164c7e2bacda4729da (diff) | |
| download | genenetwork2-82922e5a052abf22b9d458ddebaf8ee523bd6f55.tar.gz | |
Use external process to compute sample correlations
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 15 |
1 files changed, 6 insertions, 9 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index caa9b619..fe05635e 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -11,7 +11,7 @@ from base import data_set from base.trait import create_trait from base.trait import retrieve_sample_data -from gn3.computations.correlations import compute_all_sample_correlation +from gn3.commands import run_sample_corr_cmd from gn3.computations.correlations import fast_compute_all_sample_correlation from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import compute_all_lit_correlation @@ -108,9 +108,9 @@ def sample_for_trait_lists(corr_results, target_dataset, (this_trait_data, target_dataset) = fetch_sample_data( start_vars, this_trait, this_dataset, target_dataset) - correlation_results = compute_all_sample_correlation(corr_method="pearson", - this_trait=this_trait_data, - target_dataset=target_dataset) + correlation_results = run_sample_corr_cmd( + corr_method="pearson", this_trait=this_trait_data, + target_dataset=target_dataset) return correlation_results @@ -211,9 +211,8 @@ def compute_correlation(start_vars, method="pearson", compute_all=False): if corr_type == "sample": (this_trait_data, target_dataset_data) = fetch_sample_data( start_vars, this_trait, this_dataset, target_dataset) - - correlation_results = compute_all_sample_correlation( - corr_method=method, this_trait=this_trait_data, target_dataset=target_dataset_data) + correlation_results = run_sample_corr_cmd( + method, this_trait_data, target_dataset_data) elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") @@ -275,12 +274,10 @@ def compute_corr_for_top_results(start_vars, target_dataset, corr_type): if corr_type != "tissue" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet": - tissue_result = tissue_for_trait_lists( correlation_results, this_dataset, this_trait) if tissue_result: - correlation_results = merge_correlation_results( correlation_results, tissue_result) |