# Trouble Reading .h5 files

**URL:** <https://discourse.scverse.org/t/trouble-reading-h5-files/1288>\
**Category:** scanpy\
**Created:** [April 6, 2023, 7:27pm UTC](https://discourse.scverse.org/t/trouble-reading-h5-files/1288 "2023-04-06T19:27:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jjeang](https://avatars.discourse-cdn.com/v4/letter/j/7ba0ec/32.png) [@jjeang](https://discourse.scverse.org/u/jjeang)\
**Post date:** [April 6, 2023, 7:27pm UTC](https://discourse.scverse.org/t/trouble-reading-h5-files/1288/1 "2023-04-06T19:27:02Z")

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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

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<div class="post-metadata">

**Author:** ![gtca](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/gtca/32/1199_2.png) [@gtca](https://discourse.scverse.org/u/gtca)\
**Post date:** [April 13, 2023, 5:42pm UTC](https://discourse.scverse.org/t/trouble-reading-h5-files/1288/2 "2023-04-13T17:42:47Z")

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Hey @jjeang,

Does this .h5 file follow the expected structure for [HDF5 files from 10x Genomics](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)?

In case it’s a custom file, you should be able to read its contents with `h5py` and then use the data to construct an AnnData object. Is it something that you expect to fit in memory (you can see the dimensions without loading the dataset)?