For a list of files I am using this array on linux:

lines=$(wc -l input.txt|cut -f 1 -d ' ')
for i in $(eval echo {1..$lines}); do
name=$(head -n $i  input.txt|tail -n 1 |cut -f 1)
var1=$(head -n $i  input.txt|tail -n 1 |cut -f 2)
var2=$(head -n $i  input.txt|tail -n 1 |cut -f 3)
input=$(echo ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX239/$var1/$var2/$var2.sra)
wget -I $input -O $name
done

Thank you for your help!