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authorzsloan2022-10-14 23:21:52 +0000
committerzsloan2022-10-14 23:22:12 +0000
commit14c3ffbbc27fc94b56c446ae215ff561593b62c7 (patch)
treedba2521050ebc254aced7355b3269335524b5e3d
parent9a2949d3a3fda12fe6b48ce1fdd8b23eff274e1d (diff)
downloadgenenetwork2-14c3ffbbc27fc94b56c446ae215ff561593b62c7.tar.gz
Add redis_conn as argument to get_samplelist calls
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py3
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py3
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(":")