DENGUE Pipeline Notes

Upload documents to VDB

1. Download sequences from LANL
   • Select GB Submission Date >=MM/YYYY of last VDB update or "Last GenBank Update" in the upper right corner (whichever is earlier).
   • Set the rest of the parameters as shown:
     
     
   • Hit "Search"
     
   • Select "Save Background Info" and check the box for "Click here to include the sequence."
     
2. Move downloaded file to fauna/data
3. Upload to vdb database
   • python vdb/dengue_upload.py -db vdb -v dengue --fname results.tbl --ftype tsv

Download sequence documents from VDB

• python vdb/dengue_download.py # all serotypes together
• python vdb/dengue_download.py --select serotype:1 # just serotype 1
• python vdb/dengue_download.py --select serotype:2 # just serotype 2
• python vdb/dengue_download.py --select serotype:3 # just serotype 3
• python vdb/dengue_download.py --select serotype:4 # just serotype 4

Download titer documents from TDB

• python tdb/download.py -db tdb -v dengue --fstem dengue