Reputation: 1
I have a (hopefully) quick question for you this morning. Whenever I use the sc.read_10x_mtx (and below is my text block) I get the following error.
adata = sc.read_10x_mtx(
'filtered_feature_bc_matrix_folder/',
var_names='gene_symbols',
cache=True)
TypeError Traceback (most recent call last)
Cell In[11], line 1
----> 1 adata = sc.read_10x_mtx(
2 'filtered_feature_bc_matrix_folder/',
3 var_names='gene_symbols',
4 cache=True)
File ~/anaconda3/lib/python3.10/site-packages/scanpy/readwrite.py:491, in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only, prefix)
489 prefix = "" if prefix is None else prefix
490 is_legacy = (path / f"{prefix}genes.tsv").is_file()
--> 491 adata = _read_10x_mtx(
492 path,
493 var_names=var_names,
494 make_unique=make_unique,
495 cache=cache,
496 cache_compression=cache_compression,
497 prefix=prefix,
498 is_legacy=is_legacy,
499 )
500 if is_legacy or not gex_only:
501 return adata
File ~/anaconda3/lib/python3.10/site-packages/scanpy/readwrite.py:533, in _read_10x_mtx(path, var_names, make_unique, cache, cache_compression, prefix, is_legacy)
531 var_names_idx = pd.Index(genes[1].values)
532 if make_unique:
--> 533 var_names_idx = anndata.utils.make_index_unique(var_names_idx)
534 adata.var_names = var_names_idx
535 adata.var["gene_ids"] = genes[0].values
File ~/anaconda3/lib/python3.10/site-packages/anndata/utils.py:250, in make_index_unique(index, join)
248 while True:
249 counter[v] += 1
--> 250 tentative_new_name = v + join + str(counter[v])
251 if tentative_new_name not in values_set:
252 values_set.add(tentative_new_name)
TypeError: unsupported operand type(s) for +: 'float' and 'str'
Just hopeful for any advice! Thank you very much.
Using sc.read_10x_mtx and having my data properly import from 10x matrix software
Upvotes: 0
Views: 387