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waldronlab / bedbaser

An R client for bedbase.org
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standardize cache dir setting #3

Open nsheff opened 1 day ago

nsheff commented 1 day ago

Two suggestions on cache dir:

  1. I like the ability to configure via env var. Should we use the same env var for the python client? we're using BBCLIENT_CACHE. Maybe just standardize both packages on BEDBASE_CACHE?
  2. It would be nice to be able to configure the cache dir without an env var, if desired. maybe parameterize it through the constructor api = BEDbase(cache_dir="...")? This way I could have 2 apis pointing at different services, for instance, or maybe I don't want to or cant set an env var for some reason.
jwokaty commented 1 day ago

Great suggestions, thanks!

sanghoonio commented 1 day ago

Is it worth adding an export function so you can save the bed files from a bed ID or bedset to a directory of your choice? Or maybe you could include cache_dir as a param for bb_to_granges/list() so you can set where the bed files are saved individually?