DENGUE Pipeline Notes
Upload documents to VDB
- Download sequences from LANL
- Select GB Submission Date
>=MM/YYYYof 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."
- Select GB Submission Date
- Move downloaded file to
fauna/data - 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 togetherpython vdb/dengue_download.py --select serotype:1# just serotype 1python vdb/dengue_download.py --select serotype:2# just serotype 2python vdb/dengue_download.py --select serotype:3# just serotype 3python 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