Download the latest SARS-CoV-2 sequences from RefSeq and GenBank

covid.sh

#!/bin/bash

# Functions
download() { echo -e "Saving output to file: $1"; curl --http1.1 --retry 5 --verbose -L 'https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc&dlfmt=fasta&fl=id,Definition_s,Nucleotide_seq' > "$1" || echo 'Download failed... please try again!'; }
echoerr() { cat <<< "$@" 1>&2; }
help() { cat << EOF

Download the latest SARS-CoV-2 sequence from GeneBank and RefSeq. Please note that providing 
the output filename of the downloaded sequences is optional. 

USAGE:
    covid [OPTIONS] download [output_filename.fa]

Positional Arguments:
    [1]    download          Downloads the latest SARS-CoV-2 sequences from GenBank and GenBank
    [2]    output_filename   Optional output filename of the downloaded sequences 

OPTIONS:
    -h,    --help    Displays usage and help information    

Examples:
    covid  download  # output filename will default to covid-19_sequences_$timestamp.fa
    covid  download  covid-19_latest_sequences.fa

EOF
}

# Main Method
timestamp=$(date '+%Y-%m-%d-%H-%M')
oname="${2:-covid-19_sequences_${timestamp}.fa}" # Setting default output fname to covid-19_sequences_${timestamp}.fa

# Trap to catch SIGINT and delete output file
trap "echo; rm -f $oname" INT

# Parse sub-commands 
case "$1" in 
    download) download "$oname";;
    help) help && exit 0;;
    -h) help && exit 0;;
    --help) help && exit 0;;
    *) echoerr "ERROR: Failed to provide vaild usage of $0"; help; exit 1;;
esac