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authorAlexander Kabui2021-11-11 15:56:31 +0300
committerAlexander Kabui2021-11-11 15:56:31 +0300
commit6ced33f201e8a4e389a077a91ba9ed8bf5c19fa0 (patch)
treeea5bbd67e2053ce3a9ce1a4a3c7890aa4420dd66
parentbbc75dcef80c3df600ab01c1804a27cdfdce1b80 (diff)
downloadgenenetwork2-6ced33f201e8a4e389a077a91ba9ed8bf5c19fa0.tar.gz
fix issue with number for samples
-rw-r--r--wqflask/wqflask/correlation/pre_computes.py37
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