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/GenomicFastaResults.fasta - Upload to vdb database
python2 vdb/dengue_upload.py -db vdb -v dengue --source genbank --locus genome --fname GenomicFastaResults.fasta
Update
- Update citation fields
python2 vdb/dengue_update.py -db vdb -v dengue --update_citations- updates
authors,title,url,journalandpuburlfields from genbank files - If you get
ERROR: Couldn't connect with entrez, please run againjust run command again
Download sequence documents from VDB
python2 vdb/dengue_download.py# all serotypes togetherpython2 vdb/dengue_download.py --select serotype:dengue_virus_1# just serotype 1python2 vdb/dengue_download.py --select serotype:dengue_virus_2# just serotype 2python2 vdb/dengue_download.py --select serotype:dengue_virus_3# just serotype 3python2 vdb/dengue_download.py --select serotype:dengue_virus_4# just serotype 4
Download titer documents from TDB
python2 tdb/download.py -db tdb -v dengue --fstem dengue