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bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline
BSD 3-Clause "New" or "Revised" License
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Add support for NCBI Datasets project #96

Closed misialq closed 1 year ago

misialq commented 3 years ago

As a RESCRIPt user, I want the NCBI's datasets/dataformat command-line tools support in RESCRIPt so that I can easily download annotated genomes and their metadata by taxon/taxon ID.

See here: https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-start/ And here some usage examples for viral genomes: https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-virus/

misialq commented 3 years ago

As it turns out, there's also an existing python package: https://pypi.org/project/ncbi-datasets-pylib/ And some documentation here: https://github.com/ncbi/datasets/tree/master/client_docs/python

Also, here some usage examples can be found in a form of Jupyter notebooks.

nbokulich commented 1 year ago

closed by #153

(@misialq please reopen if I missed something)