Rethink database to support real-time virus analysis

ZIKA Pipeline Notes

Update

  • Update citation fields
    • python vdb/zika_update.py -db vdb -v zika --update_citations
    • updates authors, title and url 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, latitude, longitude 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

ZiBRA sequences

  • Replace ^>([^|]+)\|([^|]+)\|([^|]+)\|([^|]+)\|(\S+) .+ with >\1|\1|\5|brazil|\4|\3
  • Replace ^>([^|]+)\|\d.+ with >\1|\1|XXXX-XX-XX|brazil|brazil|brazil

Upload with:

python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Good.fasta --url https://github.com/zibraproject/zibraproject.github.io/tree/master/data/consensus
python vdb/zibra_upload.py -db vdb -v zika --source zibra --locus genome --authors "Zika in Brazil Real-time Analysis Consortium" --fname BRA_ZIBRA_Partial.fasta --url https://github.com/zibraproject/zibraproject.github.io/tree/master/data/consensus

Scripps sequences

  • Replace: ^>([^|]+)\|XX\| with >\1|\1|

Upload with:

python vdb/zibra_upload.py -db vdb -v zika --source andersen --locus genome --authors "Grubaugh et al" --fname andersen.fasta

Broad sequences

  • Replace: [date_omitted_pending_approval] with 2016-XX-XX
  • Replace South_Brazil with brazil
  • Replace: >([^\|]+)\|([^\|]+)\|(\S+)\r with >\1|\1|ZIKV|\3|human|\2\r
  • Curate host in samples that have MOS in the name

Upload with:

python vdb/zika_upload.py -db vdb -v zika --source broad --locus genome --authors "Broad Viral Genomics Group" --fname sequences-generated-in-this-study.fasta --url http://biorxiv.org/content/early/2017/02/18/109348

USAMRIID sequences

  • Replace: ^>([^_]+)_[^_]+_[^_]+_(\S+) with >\1|\1|\2|human|usa|florida|florida

Upload with:

python vdb/zibra_upload.py -db vdb -v zika --source usamriid --locus genome --authors "Ladner et al" --fname RIID_ZIKV_FL_10-27-16.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-seq/tree/master/consensus-genomes
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-seq/tree/master/consensus-genomes