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grst/airr-json.ipynb

Created June 13, 2023 17:55
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grst commented Jul 23, 2023

This is a prototype of a streaming parser of the AIRR JSON format leveraging the ijson library.

It takes ~35 seconds on my laptop to create a mudata object including gene expression and
AIRR data on my laptop.

What is currently not handled properly is the sample-level metadata. It is just dumped as a json string
in mudata.uns["metadata"]​. Ann/MuData doesn't have the concept of having sample rather than cell metadata.
I think for now the best solution would be to transfer the metadata of interest (say, the patient's sex and age) to
adata.obs​ as cell-level metadata. Since this will be stored as categoricals, it will be quite space efficent, also for larger datasets.

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grst commented Jul 23, 2023

Tagging @bcorrie here, since I'm still unsure if you received my email.

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