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-rw-r--r--gn3/db/correlations.py20
1 files changed, 11 insertions, 9 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index d372607..3ae66ca 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -26,9 +26,9 @@ def get_filename(conn: Any, target_db_name: str, text_files_dir: str) -> Union[
(target_db_name,))
result = cursor.fetchone()
if result:
- filename = "ProbeSetFreezeId_{tid}_FullName_{fname}.txt".format(
- tid=result[0],
- fname=result[1].replace(' ', '_').replace('/', '_'))
+ filename = (
+ f"ProbeSetFreezeId_{result[0]}_FullName_"
+ f"{result[1].replace(' ', '_').replace('/', '_')}.txt")
full_filename = f"{text_files_dir}/{filename}"
return (
os.path.exists(full_filename) and
@@ -53,7 +53,7 @@ def build_temporary_literature_table(
query = {
"rat": "SELECT rat FROM GeneIDXRef WHERE mouse=%s",
"human": "SELECT human FROM GeneIDXRef WHERE mouse=%d"}
- if species in query.keys():
+ if species in query:
cursor.execute(query[species], row[1])
record = cursor.fetchone()
if record:
@@ -160,8 +160,10 @@ def fetch_symbol_value_pair_dict(
symbol: data_id_dict.get(symbol) for symbol in symbol_list
if data_id_dict.get(symbol) is not None
}
- query = "SELECT Id, value FROM TissueProbeSetData WHERE Id IN ({})".format(
- ",".join(f"%(id{i})s" for i in range(len(data_ids.values()))))
+ data_ids_fields = (f"%(id{i})s" for i in range(len(data_ids.values())))
+ query = (
+ "SELECT Id, value FROM TissueProbeSetData "
+ f"WHERE Id IN ({','.join(data_ids_fields)})")
with conn.cursor() as cursor:
cursor.execute(
query,
@@ -408,12 +410,12 @@ def fetch_sample_ids(
`web.webqtl.correlation.CorrelationPage.fetchAllDatabaseData` function in
GeneNetwork1.
"""
+ samples_fields = (f"%(s{i})s" for i in range(len(sample_names)))
query = (
"SELECT Strain.Id FROM Strain, Species "
- "WHERE Strain.Name IN ({}) "
+ f"WHERE Strain.Name IN ({','.join(samples_fields)}) "
"AND Strain.SpeciesId=Species.Id "
- "AND Species.name=%(species_name)s").format(
- ",".join(f"%(s{i})s" for i in range(len(sample_names))))
+ "AND Species.name=%(species_name)s")
with conn.cursor() as cursor:
cursor.execute(
query,