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Expose 'raw' as an argument?

Open Yaoyx opened this issue 2 years ago • 2 comments

https://github.com/calico/basenji/blob/615b9eec8a591783b16d959029ddad08edae853d/basenji/dataset.py#L215

It currently returns index format for dna sequence as default. Should this be exposed in case hdf5 file has index format, which seems to be the default (https://github.com/calico/basenji/blob/615b9eec8a591783b16d959029ddad08edae853d/bin/basenji_data_write.py#L157)

This would, for example, make the explore_model.ipynb data loading consistent with the input shape and format required for a model prediction.

Yaoyx avatar Aug 10 '23 21:08 Yaoyx

I won't have time to look into this for awhile. It sounds like you understand what ought to happen, so feel free to submit a pull request.

davek44 avatar Aug 13 '23 21:08 davek44

I won't have time to look into this for awhile. It sounds like you understand what ought to happen, so feel free to submit a pull request.

Sounds good. I just submitted a pull request.

Yaoyx avatar Aug 16 '23 00:08 Yaoyx