Some troubles with Loading data

[XUEbaogai0101]

Hi Dr.Qiu,
I met problem when I use dyn.read() to read my loom data, which was processing by velocyto and run sucessfully in scvelo.
But it seems that something wrong with my data, but I don' know how to fix it.
Error shows as following:

`
adata = dyn.read('WT.loom')
TypeError Traceback (most recent call last)
/tmp/ipykernel_1760149/501344354.py in
----> 1 adata = dyn.read('WT.loom')

~/miniconda3/envs/dynamo/lib/python3.7/site-packages/anndata/_io/h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
440 _clean_uns(d) # backwards compat
441
--> 442 return AnnData(**d)
443
444

TypeError: init() got an unexpected keyword argument 'attrs'
`

And I find some problems when I read a concatenated anndata as well which also was processing by velocyto and I didn't process it.

`adata = scv.read('WT.loom', cache=True)
ldata = scv.read('WC.loom', cache=True)
aaa=adata.concatenate(ldata,join='outer')
aaa.write('WT_WC_.h5ad',compression="gzip")
adata = dyn.read('WT_WC_.h5ad')

KeyError Traceback (most recent call last)
~/miniconda3/envs/dynamo/lib/python3.7/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
155 try:
--> 156 return func(elem, *args, **kwargs)
157 except Exception as e:

~/miniconda3/envs/dynamo/lib/python3.7/site-packages/anndata/_io/h5ad.py in read_group(group)
531 if encoding_type:
--> 532 EncodingVersions[encoding_type].check(
533 group.name, group.attrs["encoding-version"]

~/miniconda3/envs/dynamo/lib/python3.7/enum.py in getitem(cls, name)
356 def getitem(cls, name):
--> 357 return cls.member_map[name]
358

KeyError: 'dict'

During handling of the above exception, another exception occurred:

AnnDataReadError Traceback (most recent call last)
/tmp/ipykernel_1760149/353394512.py in
----> 1 adata = dyn.read('WT_WC_.h5ad')

~/miniconda3/envs/dynamo/lib/python3.7/site-packages/anndata/_io/h5ad.py in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
424 d[k] = read_dataframe(f[k])
425 else: # Base case
--> 426 d[k] = read_attribute(f[k])
427
428 d["raw"] = _read_raw(f, as_sparse, rdasp)

~/miniconda3/envs/dynamo/lib/python3.7/functools.py in wrapper(*args, **kw)
838 '1 positional argument')
839
--> 840 return dispatch(args[0].class)(*args, **kw)
841
842 funcname = getattr(func, 'name', 'singledispatch function')

~/miniconda3/envs/dynamo/lib/python3.7/site-packages/anndata/_io/utils.py in func_wrapper(elem, *args, **kwargs)
161 parent = _get_parent(elem)
162 raise AnnDataReadError(
--> 163 f"Above error raised while reading key {elem.name!r} of "
164 f"type {type(elem)} from {parent}."
165 )

AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.
`

Thank you very much!
XUE

[XUEbaogai0101]

I find some answers about the concatenated anndata, it seems that the format of an AnnData objects stored on disk is updated in the latest version.
scverse/anndata#698 (comment)

[Xiaojieqiu]

Hi @XUEbaogai0101 thanks for using dynamo. You are right, this is an anndata version issue. what is your anndata version?

also have you tried to use adata = dyn.read_loom('WT.loom')?

[XUEbaogai0101]

Hi Dr.Qiu!@Xiaojieqiu
Thank you for answering my question. My anndata version is 0.8.0.
I tried the use of read_loom, it worked. What a simple question, I am sorry for my sloppiness.
Thanks for your generous answer again.