Remove to-dos, handle lint warnings and run notebooks #20
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KoalaQin
changed the title
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| # TODO: Are there other things we want to store in a session? Like a PASS variants only | |||
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Can you add this to a ticket so we don't forget?
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| from gnomad_toolbox.load_data import _get_dataset, get_compatible_dataset_versions | |||
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| # TODO: Check these csq sets, the ones in the code don't match what is listed on the | |||
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Can you confirm these csq sets? I forgot about this TODO, but I think we need to make sure they are consistent. I copied the doc string csqs from the browser hover over, but I just used the csqs that you had in your original code. If the code is correct, can you just change the doc string?
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I asked the browser people if it's hard coded or the list includes all the csqs for different VEP versions (there are some new csq 105 csq not shown there), but for now I changed a bit the code and the docstring, so it's doing what it's saying.
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It looks like it's hardcoded for 'Other' and they didn't update the list by VEP version, so we might have a different number for that category but it should be rare (I assume those deprecated/added are not so common), for now, our code is aligned to their LoF, missense and synonymous.
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| from gnomad_toolbox.load_data import _get_dataset, get_compatible_dataset_versions | |||
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| # TODO: Check these csq sets, the ones in the code don't match what is listed on the | |||
| @@ -115,8 +115,6 @@ | |||
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| # TODO: Are there other things we want to store in a session? Like a PASS variants only | |||
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