ENH: get_rdp_data

[mikerobeson]

Even though there is an avenue for QIIME 2 users to obtain and import premade RDP files for use in taxonomy assignment. Some users may like to curate the RDP database themselves. This code will provide that ability, while also extracting additional taxonomic rank information not currently available from the premade QIIME 2 compatible RDP files.

The full RDP data is available here, and contains the latest information as per the 08/14/2020 RDP release notes.

Currently this draft includes:

• two actions:
  • parse-rdp-taxonomy
  • optionally add species labels (e.g. like get-silva-data)
  • optionally propagate taxonomic ranks
  • choose ranks of interest
  • get-rdp-data
  • wraps parse-rdp-taxonomy under the hood
  • downloads both Archaea and Bacteria (16S rRNA gene data) together
  • downloads Fungi (28S rRNA gene data)

TODO:

• [ ] add ability to download the Archaea and Bacteria domains individually
• [ ] add ability to download aligned sequences
• [ ] write test code
• [ ] consider refactoring the get_rdp_data function and associated code to resemble get_gtdb_data

[mikerobeson]

I was notified that there was a discontinuation of funding for RDP. I followed up with the user privately, and it does seem to be the case. This also explains why the http://rdp.cme.msu.edu/ website has been down. However, it does appear the associated sourceforge and GitHub sites will remain.

For this reason I'll be closing this PR. :-(

[nbokulich]

ah too bad! thanks @mikerobeson !