How can I obtain FTP links to studies in ENA? How can I programmatically obtain ftp links to RNA seq fastq files in ENA? Here's an example of a link that I would be interested in obtaining:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR824/000/SRR8240860/SRR8240860_1.fastq.gz
In particular, is there some tool that, given the BioProject ID (here, PRJNA506829), would be able give me all ftp links for the runs in the project, or would I need to write a web scraper to do it?
Here are some command lines I used for that purpose in bash.
Simply prepare a text file containing each accession number (SRR/ERR) you want and create a for loop. Here I used prozilla to speed up downloads but you may use wget either.
for index in $(cat list_of_accessions) ; do

if [ ${#index} -eq 9 ]; then
            proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/${index}/${index}_1.fastq.gz
            proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/${index}/${index}_2.fastq.gz
            else
            if [ ${#index} -eq 10 ]; then
                    proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/00${index:9:9}/${index}/${index}_1.fastq.gz
                            proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/00${index:9:9}/${index}/${index}_2.fastq.gz
                    else
                    if [ ${#index} -eq 11 ]; then
                     proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/0${index:9:10}/${index}/${index}_1.fastq.gz
                                        proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/0${index:9:10}/${index}/${index}_2.fastq.gz
                    else
                        proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/${index:9:11}/${index}/${index}_1.fastq.gz
                                                proz -k=6 --no-curses ftp.sra.ebi.ac.uk/vol1/fastq/${index:0:6}/${index:9:11}/${index}/${index}_2.fastq.gz
                        fi
                fi
            
            fi
done
```