[Bug] Xenium Prime - empty codewords included in the SOPA output

[wlason]

Description

After running SOPA on my dataset, both the Xenium explorer file and the report contain codewords for non-genes including:

• DeprecatedCodeword
• Intergenic_Region
• NegControlCodeword
• NegControlProbe
• UnassignedCodeword

Reproducing the issue

Run SOPA pipeline on Xenium Prime dataset.

Expected behavior

These codewords to be removed.

[quentinblampey]

Hi @wlason,

Indeed, right now, I'm not filtering these genes. I'll need a new feature from SpatialData (expected in mid-november) to be able to work on this. More details: it'll give us the capability to store some attributes at the SpatialData level, which we'll use to store a regex pattern when using sopa.io.xenium.

This is already on my to-do list, but it will not come before the end of November!