diff options
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 37 |
1 files changed, 27 insertions, 10 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index 1db9f61b..f1c9e1bd 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -6,12 +6,14 @@ import json from typing import List from base import data_set +from gn3.computations.correlations import compute_all_sample_correlation from gn3.computations.correlations import fast_compute_all_sample_correlation from gn3.computations.correlations import map_shared_keys_to_values + def get_dataset_dict_data(dataset_obj): """function to get the dataset data mapped to key""" - dataset_obj.get_trait_data() + dataset_obj.get_trait_data(dataset_obj.group.all_samples_ordered()) return map_shared_keys_to_values(dataset_obj.samplelist, dataset_obj.trait_data) @@ -42,11 +44,21 @@ def pre_compute_sample_correlation(base_dataset: List, precaution:function is expensive;targets only Exon and """ + results = [] + for trait_info in base_dataset: - yield fast_compute_all_sample_correlation(corr_method="pearson", - this_trait=trait_info, - target_dataset=target_dataset) + result = fast_compute_all_sample_correlation(corr_method="pearson", + this_trait=trait_info, + target_dataset=target_dataset) + + # results.append(fast_compute_all_sample_correlation(corr_method="pearson", + # this_trait=trait_info, + # target_dataset=target_dataset)) + print("finished") + print(result) + + return results def cache_to_file(base_dataset_name: str, target_dataset_name: str): @@ -57,16 +69,21 @@ def cache_to_file(base_dataset_name: str, target_dataset_name: str): base_dataset_data, target_dataset_data = [list(dataset) for dataset in list( fetch_datasets(base_dataset_name, target_dataset_name))] + # print(target_dataset_data) try: - with open("unique_file_name.json", "w") as file_handler: - file_handler.write() - - dataset_correlation_results = list(pre_compute_sample_correlation( - base_dataset_data, target_dataset_data)) + # with open("unique_file_name.json", "w") as file_handler: + # file_handler.write() + dataset_correlation_results = pre_compute_sample_correlation( + base_dataset_data, target_dataset_data) print(dataset_correlation_results) - json.dump(dataset_correlation_results, file_handler) + # json.dump(dataset_correlation_results, file_handler) except Exception as error: raise error + + +def check_cached_files_validity(): + """function to check the validity of cached files""" + pass |