ENH: Adds NCBI api-key option

bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

BSD 3-Clause "New" or "Revised" License

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ENH: Adds NCBI api-key option #203

Closed mikerobeson closed 2 months ago

mikerobeson commented 2 months ago

Attempts to fix #145, by adding the --p-api-key option to both get-ncbi-data and get-ncbi-data-protein. It does this by appending api_key to the _entrez_params dictionary so that it is available for all NCBI requests.

To do:

Test code
- I could use help on the best way to write test code for this...
- Might test reading in a mock api-key?

mikerobeson commented 2 months ago

Going to close this PR as it is clear that NCBI requests are not the rate-limiting step. At least for the purposes being used here. This was confirmed after several rounds of testing. There was no difference in overall run time when downloading marker gene data from NCBI, with or without the api-key.