debugged the biomart issue

scdataloader/utils.py

@@ -127,15 +127,15 @@ def getBiomartTable(
 
     cache_folder = os.path.expanduser(cache_folder)
     createFoldersFor(cache_folder)
-    cachefile = os.path.join(cache_folder, ".biomart.csv")
+    cachefile = os.path.join(cache_folder, ".biomart.parquet")
     if useCache & os.path.isfile(cachefile):
         print("fetching gene names from biomart cache")
-        res = pd.read_csv(cachefile)
+        res = pd.read_parquet(cachefile)
     else:
         print("downloading gene names from biomart")
 
         res = _fetchFromServer(ensemble_server, attr + attributes, database=database)
-        res.to_csv(cachefile, index=False)
+        res.to_parquet(cachefile, index=False)
     res.columns = attr + attributes
     if type(res) is not type(pd.DataFrame()):
         raise ValueError("should be a dataframe")
@@ -368,7 +368,14 @@ def load_genes(organisms: Union[str, list] = "NCBITaxon:9606"):  # "NCBITaxon:10
         genesdf["organism"] = organism
         organismdf.append(genesdf)
     organismdf = pd.concat(organismdf)
-    for col in ["source_id", "run_id", "created_by_id", "updated_at", "stable_id", "created_at"]:
+    for col in [
+        "source_id",
+        "run_id",
+        "created_by_id",
+        "updated_at",
+        "stable_id",
+        "created_at",
+    ]:
         if col in organismdf.columns:
             organismdf.drop(columns=[col], inplace=True)
     return organismdf

tests/test_base.py

@@ -45,6 +45,7 @@ def test_base():
             how="most expr",  # for the collator (most expr genes only will be selected)
             max_len=1000,  # only the 1000 most expressed
             batch_size=64,
+            do_gene_pos=False,
             num_workers=1,
             clss_to_weight=["organism_ontology_term_id", "cell_type_ontology_term_id"],
             clss_to_pred=["organism_ontology_term_id", "cell_type_ontology_term_id"],