Open tyleraland opened 8 years ago
FYI Noah and I have a version of bioy ncbi_fetch
called deenurp ncbi_extract_genbank
that maybe we can combine efforts on: https://github.com/fhcrc/deenurp/blob/master/deenurp/subcommands/ncbi_extract_genbank.py
I'll look into using that instead, since ncbi_fetch has a pretty limited scope anyway. Thanks.
deenurp has enough dependencies that it seems like a significant hassle to include it in my pipeline. So I'd prefer one of:
After some tinkering I got deenurp installed with very few dependencies and enough functionality to run ncbi_extract_genbank. I'll monkey around with it.
Seems to work and I like it. I'd vote to just ditch bioy ncbi_fetch entirely and consolidate efforts into deenurp.
Allegedly GI identifiers are going away in June and switching to "accessioned" gb identifiers: https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
So ncbi_fetch should require gb's