ZIKA Pipeline Notes
Download
python3 vdb/zika_download.py -db vdb -v zika --fstem zika --resolve_method choose_genbank
Upload
ViPR sequences
- 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
- Move downloaded sequences to
fauna/data - Upload to vdb database
python3 vdb/zika_upload.py -db vdb -v zika --source genbank --locus genome --fname GenomicFastaResults.fasta
Fred Hutch sequences
Upload with:
python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands" --fname zika_usvi_good.fasta
python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands" --fname zika_usvi_partial.fasta
python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-colombia/ --title "Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia" --fname ZIKA-COL-good.fasta
python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-colombia/ --title "Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia" --fname ZIKA-COL-partial.fasta
Update
- Update citation fields
python2 vdb/zika_update.py -db vdb -v zika --update_citations- updates
authors,title,url,journalandpuburlfields from genbank files - If you get
ERROR: Couldn't connect with entrez, please run againjust run command again