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| author | zsloan | 2022-10-14 23:21:52 +0000 |
|---|---|---|
| committer | zsloan | 2022-10-14 23:22:12 +0000 |
| commit | 14c3ffbbc27fc94b56c446ae215ff561593b62c7 (patch) | |
| tree | dba2521050ebc254aced7355b3269335524b5e3d /wqflask | |
| parent | 9a2949d3a3fda12fe6b48ce1fdd8b23eff274e1d (diff) | |
| download | genenetwork2-14c3ffbbc27fc94b56c446ae215ff561593b62c7.tar.gz | |
Add redis_conn as argument to get_samplelist calls
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 3 |
2 files changed, 4 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 08a38527..4420796c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -7,6 +7,7 @@ import json from base import webqtlConfig from base.trait import create_trait from base.data_set import create_dataset +from utility.redis_tools import get_redis_conn from utility.tools import flat_files, assert_file from utility.tools import GEMMA_WRAPPER_COMMAND from utility.tools import TEMPDIR @@ -163,7 +164,7 @@ def gen_covariates_file(this_dataset, covariates, samples): trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) - this_dataset.group.get_samplelist() + this_dataset.group.get_samplelist(redis_conn=get_redis_conn()) trait_samples = this_dataset.group.samplelist trait_sample_data = trait_ob.data for index, sample in enumerate(trait_samples): diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 1fca5468..9a42bc35 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -13,6 +13,7 @@ import numpy as np from base.webqtlConfig import TMPDIR from base.trait import create_trait +from utility.redis_tools import get_redis_conn from utility.tools import locate, GN3_LOCAL_URL from wqflask.database import database_connection @@ -148,7 +149,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict: """ cofactor_dict = {} if cofactors: - dataset_ob.group.get_samplelist() + dataset_ob.group.get_samplelist(redis_conn=get_redis_conn()) sample_list = dataset_ob.group.samplelist for cofactor in cofactors.split(","): cofactor_name, cofactor_dataset = cofactor.split(":") |