fixed the index error

wtsi-hgi · May 11, 2024 · 9a45fea · 9a45fea
1 parent cf87ee4
commit 9a45fea
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/bin/generate_combined_celltype_anotation_file.py b/bin/generate_combined_celltype_anotation_file.py
@@ -127,13 +127,13 @@ def main():
         adata1 = scanpy.read_h5ad(ad1)
         if adata1.n_obs > 0:
             adatasets.append(adata1)
-    ad = adatasets[0].concatenate(*adatasets[1:])
-    if(len(adatasets)>1):
-        # in this case the concentration adds a -1 -2 -3 to index that has to be removed.
-        all_index = pd.DataFrame(ad.obs.index,columns=['col'])
-        all_indexes = all_index['col'].str.split('-')
-        all_together = all_indexes.str[0]+'-'+all_indexes.str[1]+'-'+all_indexes.str[2]
-        ad.obs.set_index(all_together, inplace=True)
+    ad = adatasets[0].concatenate(*adatasets[1:],index_unique=None)
+    # if(len(adatasets)>1):
+    #     # in this case the concentration adds a -1 -2 -3 to index that has to be removed.
+    #     all_index = pd.DataFrame(ad.obs.index,columns=['col'])
+    #     all_indexes = all_index['col'].str.split('-')
+    #     all_together = all_indexes.str[0]+'-'+all_indexes.str[1]+'-'+all_indexes.str[2]
+    #     ad.obs.set_index(all_together, inplace=True)
 
     # ad2 = adatasets2[0].concatenate(*adatasets2[1:])
     # ad = scanpy.read(adata)