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I started using scanny to read in data, but I always got the following error. I can't find any other detailed reasons. #3355

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xzt199610 opened this issue Nov 12, 2024 · 0 comments

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@xzt199610
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adata = sc.read_10x_mtx(
'/mnt/d/02PhD/A03Data_Analysis/B02单细胞数据/01单细胞数据/01PVAT/GSE275779_RAW/NC/', # the directory with the .mtx file
var_names='gene_symbols', # use gene symbols for the variable names (variables-axis index)
cache=True )


ValueError Traceback (most recent call last)
Cell In[4], line 1
----> 1 adata = sc.read_10x_mtx(
2 '/mnt/d/02PhD/A03Data_Analysis/B02单细胞数据/01单细胞数据/01PVAT/GSE275779_RAW/NC/', # the directory with the .mtx file
3 var_names='gene_symbols', # use gene symbols for the variable names (variables-axis index)
4 cache=True )

File ~/anaconda3/lib/python3.11/site-packages/legacy_api_wrap/init.py:80, in legacy_api..wrapper..fn_compatible(*args_all, **kw)
77 @wraps(fn)
78 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
79 if len(args_all) <= n_positional:
---> 80 return fn(*args_all, **kw)
82 args_pos: P.args
83 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]

File ~/anaconda3/lib/python3.11/site-packages/scanpy/readwrite.py:561, in read_10x_mtx(path, var_names, make_unique, cache, cache_compression, gex_only, prefix)
559 prefix = "" if prefix is None else prefix
560 is_legacy = (path / f"{prefix}genes.tsv").is_file()
--> 561 adata = _read_10x_mtx(
562 path,
563 var_names=var_names,
564 make_unique=make_unique,
565 cache=cache,
566 cache_compression=cache_compression,
...
375 (asstr(part.strip()) for part in line.split())
376 if not mmid.startswith('%%MatrixMarket'):
377 raise ValueError('source is not in Matrix Market format')

ValueError: too many values to unpack (expected 5)
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...

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