RethinkDB database to support real-time virus analysis

Download data from Genbank

  • Genbank search URL
  • This is search fields of measles[title] AND viruses[filter] AND ("5000"[SLEN] : "20000"[SLEN])
  • Send to : Complete Record : File : Accession List
  • This downloads the file sequence.seq
  • Open this file and remove the .1, .2, etc… from the accession numbers

Upload to fauna

python3 vdb/ -db vdb -v measles --ftype accession --source genbank --locus genome --fname sequence.seq

Download from fauna

python3 vdb/ -db vdb -v measles --fstem measles --resolve_method choose_genbank