A program to retrieve the Reference Sequence datasets for plant, insect and fungal viruses.
Keep in mind this is a beta version, bugs are expected. Program tested only in Mac and Linux OS.

First, you need to install R (version >4.0) if you don't have it.
You can use on mac brew or in linux apt get to install R.
Then, install the R libraries execute the sh installRpkg.sh install command and it will install the packages necessary to run virDB-launcher.sh.

You need to exectute virDB-launcher.sh in the command line and with an stable internet connection - otherwise, NCBI fetcher will be interrupted, and the process needs to starts again.

#You have 5 options (select a number)
#1: plants
#2: land plants
#3: invertebrates,land plants
#4: invertebrates
#5: fungi

This is an example to run virDB-launcher:

sh virDB-launcher.sh 1 # to retrieve option 1: plants

Preparing BLAST databases

makeblastdb -in Viral_nucleic_acid_database -out virusDB -dbtype nucl -hash_index

BLASTn and BLASTx

# blast nucleotides
blastn -query contigs.fasta -db virDBnt -out contigs_blastn.tsv  -num_threads 4 
# blast nucleotides x proteins
blastx -query contigs.fasta -db virDBaa -out  contigs_blastx.tsv -num_threads 4  

Note:

The NCBI entries for plant hosts were splited as plants, land plants, and viruses that infect plants and are vectored by insects as invertebrates,landplants, because this has to do with NCBI indexing. You need to download plants, land plants and invertebrates,landplants to have the FULL plants database. After downloading all the databases, you can merge your fasta files with cat plants_722.fasta, land_plants_722.fasta invertebrates,landplants_722.fasta