ZIKA Pipeline Notes

Update

• Update citation fields
  • python vdb/zika_update.py -db vdb -v zika --update_citations
  • updates authors, title, url, journal and puburl fields from genbank files
  • If you get ERROR: Couldn't connect with entrez, please run again just run command again
• Update location fields
  • After hand editing location in chateau
  • python vdb/zika_update.py -db vdb -v zika --update_locations
  • Updates division, country, region fields

Download

python vdb/zika_download.py -db vdb -v zika --fstem zika --resolve_method choose_genbank

Upload

ViPR sequences

1. Download sequences
   • Select year >= 2013 and genome length >= 5000
   • Download as Genome Fasta
   • Set Custom Format Fields to 0: GenBank Accession, 1: Strain Name, 2: Segment, 3: Date, 4: Host, 5: Country, 6: Subtype, 7: Virus Species
2. Move downloaded sequences to fauna/data
3. Upload to vdb database
   • python vdb/zika_upload.py -db vdb -v zika --source genbank --locus genome --fname GenomeFastaResults.fasta

Fred Hutch sequences

Upload with:

python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname zika_usvi_good.fasta --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands"
python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname zika_usvi_partial.fasta --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands"