I would like to obtain sample IDs that have qiita_prep_id in a list
something like
redbiom search metadata "where (qiita_prep_id in data/prep.ids)" > samples_of_interest.ids
How can I read qiita_prep_id in data/prep.ids within the search?
While this is a way to construct a list of entities to match against in a search, I do not believe this search will work. redbiom search is oriented at sample metadata that is preparation invariant. What I think is necessary instead is to find samples for your study(s) of interest, and then refine the search using "redbiom select samples-from-metadata" which accepts a --context argument and a similar type of query (e.g., the where ... piece). The use of context will require redbiom expose preparation specific information, which will include the prep ID.