diff options
Diffstat (limited to 'gn3/db/correlations.py')
| -rw-r--r-- | gn3/db/correlations.py | 20 |
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, |