Fix _index and HGNC symbol indexing

[mossjacob]

Summary 📝

Fixes a one-line bugs in the index key extraction of an AnnData store as well as the biomart processor.

Details

• Instead of accessing "_index" which does not exist as a key, access the _index attr which links to the key.

• Removes the line which limits genes to those with no HGNC symbol (is there a reason this is there?)

• Uses latest LaminDB's MappedCollection instead

[jkobject]

Hello @mossjacob,

thanks for the update! Just one question about the mapped.py update, any explanation? I take this file from lamindb's mapped function. Can you explain what it is changing?

Also, there was quite some updates recently on lamindb, if you want to update it from their version and make a PR, it would be super useful!
https://github.com/laminlabs/lamindb/blame/2e3ebeac61608f1a83f50583890db23bfec595d7/lamindb/core/_mapped_collection.py#L55

Best,

[mossjacob]

Hello @jkobject,

I think it was a bug in that line--the index of var couldn't be accessed as it was. I did not realise that this file was copied from lamin--how come you don't just import MappedCollection from lamindb? I believe lamindb is a dependency of this project?

Best,
Jacob

[jkobject]

Initially I had updates that were specific to scdataloader. Now they all got added to lamin. But I have some plans to update this part soon too so I was keeping it like this.

[mossjacob]

Hi,

I've updated the PR to use the latest Lamin mapped collection and added separately the check_aligned_vars function to the scDataLoader Dataset. How does it look to you?

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