RethinkDB database to support real-time virus analysis

Download data from VIPR

  • paramyxos -> genome search -> data to return = genome -> type "mumps" in search
  • select complete genome only (n=104 as of july 2017)
  • select all -> download
  • download genome fasta with custom format. Fields: GB-SN-SEG-DATE-HOST-COUN-SUBTY-VIRSPEC
  • copy vipr fasta file to fauna/data/mumps_vipr_full.fasta

Clean FASTA

cd fauna
python vdb/mumps_preprocess_fasta.py --vipr

The cleaned fasta is now available at data/mumps_vipr.fasta

Note: this will eventually be incorporated into the Fauna upload script

Upload to fauna

python vdb/mumps_upload.py -db vdb -v mumps --source genbank --locus genome --fname mumps_vipr.fasta

Update fauna database

This is needed to populate certain attributes such as author & paper title. python vdb/mumps_update.py -db vdb -v mumps --update_citations

Download from fauna

python vdb/mumps_download.py -db vdb -v mumps --fstem mumps --resolve_method choose_genbank