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Update all gene names #4

Closed constantinpape closed 4 years ago

constantinpape commented 4 years ago

We need to match gene names with the new prospr file names in:

I tried for the dataset already, but 2 gene names do not match up, see https://github.com/platybrowser/platybrowser-backend/blob/new-update-mechanism/misc/fixup.py#L71-L102.

vzinche commented 4 years ago

https://github.com/platybrowser/platybrowser-backend/blob/a96507900c5948ab1a9a34be74bc3b21cbf33b65/misc/new_name_lut.json#L30 https://github.com/platybrowser/platybrowser-backend/blob/a96507900c5948ab1a9a34be74bc3b21cbf33b65/misc/new_name_lut.json#L37

These two non-matching names actually originate from the renaming. So probably a cleaner way would be: if the gene_name starts with ENR or NOV, find the corresponding ENR or NOV in json

constantinpape commented 4 years ago

@vzinche I fixed the gene names in the all meds hdf5 file in a1c4056.

constantinpape commented 4 years ago

I have added the new vc profile table @vzinche made and I rerun computation for the vc assignment table. As far as I can see, all gene names are up-to-date now.