Rethink database to support real-time virus analysis

EBOLA Pipeline Notes

Upload documents to VDB

  1. Download Ebola sequence data from https://github.com/ebov/space-time/tree/master/Data
  2. Move Makona_1610_genomes_genomes.fasta sequences to fauna/data
  3. Replace SLE with sierra_leone, LBR with liberia and GIN with guinea
  4. Replace sierra_leone\|\? with sierra_leone|sierra_leone, liberia\|\? with liberia|liberia and guinea\|\? with guinea|guinea
  5. Replace sierra_leone\|\| with sierra_leone|sierra_leone|, liberia\|\| with liberia|liberia| and guinea\|\| with guinea|guinea|
  6. Upload to vdb database
    • python vdb/ebola_upload.py -db vdb -v ebola --source genbank --locus genome --fname Makona_1610_genomes_genbank.fasta
  7. Hand edit author and url info into other 153 genomes
  8. Upload to vdb database
    • python vdb/ebola_upload.py -db vdb -v ebola --source genbank --locus genome --fname Makona_1610_genomes_quick.fasta --authors "Quick et al" --url https://github.com/nickloman/ebov/

Update

  1. Update citation fields
    • python vdb/ebola_update.py -db vdb -v ebola --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

Download documents from VDB

  • python vdb/ebola_download.py -db vdb -v ebola --fstem ebola --resolve_method choose_genbank