DENGUE Pipeline Notes
Upload
ViPR sequences
- Download sequences
- Select 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 Type
- Move downloaded sequences to
fauna/data/GenomicFastaResults.fasta
cd fauna
mkdir -p data
mv ~/Downloads/GenomicFastaResults.tar.gz data/.
tar -xf data/GenomicFastaResults.tar.gz
mv data/*GenomicFastaResults.fasta data/GenomicFastaResults.fasta
- Upload to vdb database
python3 vdb/dengue_upload.py \
-db vdb \
-v dengue \
--source genbank \
--locus genome \
--fname GenomicFastaResults.fasta
Update
-
Update citation fields
python3 vdb/dengue_update.py \ -db vdb \ -v dengue \ --update_citations
- updates
authors
,title
,url
,journal
andpuburl
fields from genbank files - If you get
ERROR: Couldn't connect with entrez, please run again
just run command again
- updates
Download sequence documents from VDB
python3 vdb/dengue_download.py -v dengue
# all serotypes togetherpython3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_1
# just serotype 1python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_2
# just serotype 2python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_3
# just serotype 3python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_4
# just serotype 4
Download titer documents from TDB
python3 tdb/download.py -db tdb -v dengue --fstem dengue