ENH: action to get preformatted blast databases - Githubissues

bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

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

84 stars 25 forks source link

ENH: action to get preformatted blast databases #135

Open nbokulich opened 2 years ago

nbokulich commented 2 years ago

NCBI hosts a database of preformatted blast databases, and a tool to download these programmatically (at the moment this seems to be a perl script, update_blastdb.pl, which ships with blast+).

It would be neat to add an action to RESCRIPt for downloading these databases (basically, this would allow quick validation of the source and timestamp in provenance).

One blocker at the moment is the lack of a BLASTDB type/format in Q2 — related to https://github.com/qiime2/q2-feature-classifier/issues/158

colinbrislawn commented 4 months ago

Direct link: https://ftp.ncbi.nlm.nih.gov/blast/temp/update_blastdb.pl

Not sure if we want to wrap this script or just port part of it