Hello,
I am using
scanpy version 1.7.0 with
h5py version 3.6.0
I am trying to read a file in .h5 format (as I understand this is the legacy format). Usually this is not a problem because I can usually read:
adata = sc.read_10x_h5('my_file.h5')
and then save
adata.write_h5ad('my_file.h5ad')
However this time I am unable to read the file and get the following error
Exception: File is missing one or more required datasets.
Surprisingly (for me) I am actually able to load the file with my version of h5py
f = h5py.File('../../utils/my_file.h5', 'r')
but I just cannot access the data (e.g. load it into anndata)
There is 1 key called “shoji” and I want to access the contents of the “Expression” database which can be done through
data = f['shoji']['Expression']
But then I have trouble loading this into anndata (perhaps because it is too big but maybe because something else is wrong? My kernal dies so there is no error I can share).
I’ve also attempted sc.read_hdf('my_file.h5', key='shoji')
but then I get a counterintuitive error
TypeError: Accessing a group is done with bytes or str, not <class 'tuple'>
Suggesting that the shoji argument is a tuple instead of a string. I figure it was just a bug of a deprecated function.
Anyway, can anyone shed some light on what is happening here? Or better yet, any ideas as to how I can read this file?
Thanks