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authorzsloan2022-03-09 19:13:59 +0000
committerzsloan2022-03-16 14:41:09 -0500
commit743a4623c53d30779cb884a69d0cf2c7ff411f0a (patch)
tree671274c44dc5117ffd7b9adb8f2987aba3b440cc
parent45694eb46fa0c337d8b2f1be945bdb96c4a2af44 (diff)
downloadgenenetwork2-743a4623c53d30779cb884a69d0cf2c7ff411f0a.tar.gz
Add function for getting strain name from sample name
-rw-r--r--wqflask/maintenance/gen_ind_genofiles.py16
1 files changed, 13 insertions, 3 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py
index abca4a4a..6e818945 100644
--- a/wqflask/maintenance/gen_ind_genofiles.py
+++ b/wqflask/maintenance/gen_ind_genofiles.py
@@ -7,9 +7,7 @@ import MySQLdb
from wqflask import app
-from gn3.db.datasets import retrieve_group_samples
-
-def db_conn():
+def conn():
return MySQLdb.Connect(db=app.config.get("DB_NAME"),
user=app.config.get("DB_USER"),
passwd=app.config.get("DB_PASS"),
@@ -32,6 +30,17 @@ def main(args):
# Generate the output .geno files
generate_new_genofiles(strain_genotypes(source_genofile), target_groups)
+def get_strain_for_sample(sample):
+ query = (
+ "SELECT CaseAttributeXRefNew.Value "
+ "FROM CaseAttributeXRefNew, Strain "
+ "WHERE CaseAttributeXRefNew.CaseAttributeId=11 "
+ "AND CaseAttributeXRef.New.StrainId = Strain.Id "
+ "AND Strain.Name = %(name)s" )
+
+ with conn.cursor() as cursor:
+ return cursor.execute(query, {"name": name}).fetchone()[0]
+
def group_samples(target_group: str) -> List:
"""
Get the group samples from its "dummy" .geno file (which still contains the sample list)
@@ -115,3 +124,4 @@ def strain_genotypes(strain_genofile: str) -> List:
if __name__ == "__main__":
print("command line arguments:\n\t%s" % sys.argv)
main(sys.argv)
+