Error in samples concatenation

[ParisaMa]

Hi,

When I try to run the following line (on the case study) I receive an error:

adata.var['gene_id'] = adata.var['gene_id-1']

KeyError Traceback (most recent call last)
//anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2656 try:
-> 2657 return self._engine.get_loc(key)
2658 except KeyError:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'gene_id-1'

During handling of the above exception, another exception occurred:

KeyError Traceback (most recent call last)
in
31 # Concatenate to main adata object
32 adata = adata.concatenate(adata_tmp, batch_key='sample_id')
---> 33 adata.var['gene_id'] = adata.var['gene_id-1']
34 #adata.var.drop(columns = ['gene_id-1', 'gene_id-0'], inplace=True)
35 #adata.obs.drop(columns=['sample_id'], inplace=True)

//anaconda3/lib/python3.7/site-packages/pandas/core/frame.py in getitem(self, key)
2925 if self.columns.nlevels > 1:
2926 return self._getitem_multilevel(key)
-> 2927 indexer = self.columns.get_loc(key)
2928 if is_integer(indexer):
2929 indexer = [indexer]

//anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2657 return self._engine.get_loc(key)
2658 except KeyError:
-> 2659 return self._engine.get_loc(self._maybe_cast_indexer(key))
2660 indexer = self.get_indexer([key], method=method, tolerance=tolerance)
2661 if indexer.ndim > 1 or indexer.size > 1:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'gene_id-1'

Seems like the 'adata.concatenate' function does not create any variables as 'gene_id-1' or 'gene_id-0'. Can you please check this?

[LuckyMD]

Hi,

When posting an issue, please look up previous issues with potentially the same topic. This is addressed in issue #21. A recent Anndata update now solves an issue I was addressing with 2 lines in the script. You can now comment those out.

[ParisaMa]

Thanks!