RethinkDB database to support real-time virus analysis

Download data from Genbank

  • Genbank search URL
  • This is search fields of mumps[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

python vdb/mumps_upload.py -db vdb -v mumps --ftype accession --source genbank --locus genome --fname sequence.seq

FASTA header field ordering: 1. random numbering - this will later be filled in by GenBank accession 2. strain name 3. collection date 4. host species 5. country 6. state/region 7. genotype

Update fauna database

This is not necessary when uploading accessions as we do here. 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

Upload Broad genomes

Preprocess to fix metadata and header ordering

python vdb/mumps_preprocess_fasta.py --fasta data/muv-nextstrain-20170718.pruned.fasta > data/mumps_broad.fasta

Upload to fauna

python vdb/mumps_upload.py -db vdb -v mumps --source broad --locus genome --fname mumps_broad.fasta --authors "Wohl et al" --title "Unpublished"

Upload BCCDC genomes

If you have a FASTA file and CSV metadata, this script will help (with minor modifications as needed)

python scripts/mumps.csv-and-fasta-to-vipr-fasta.py data/input.mumps.raw.fasta data/input.mumps.csv data/input.mumps.vipr.fasta

Upload to fauna

python vdb/mumps_upload.py -db vdb -v mumps --source bccdc --locus genome --fname mumps.bc.fasta --authors "Gardy et al" --title "Unpublished"

Upload Fred Hutch genomes

Upload to fauna

python vdb/mumps_upload.py -db vdb -v mumps --source fh --locus genome --fname MuVs-WA0268502_buccal-Washington.USA-16.fasta --authors "Moncla et al" --title "Unpublished"