import subprocess
from ftplib import FTP

ftp_site = 'ftp.ncbi.nlm.nih.gov'
ftp = FTP(ftp_site)
ftp.login()
ftp.cwd('genomes/genbank/bacteria')
dirs = ftp.nlst()


for organism in dirs:
    for path in ftp.nlst(organism+"/latest_assembly_versions"):
        accession = path.split("/")[-1]
        fasta = accession+"_genomic.fna.gz"
        #print(path)
        #print(accession)
        #print(fasta)
        subprocess.call(['rsync',
                        # path is symbolically link at genomes/genbank/bacteria/organism
                        '--recursive',
                        '--copy-links',
                        '--dry-run',
                        '--include='+fasta,
                        # exclude all every dir and its contents beyond path
                        '-f=- '+path+'/**/*'
                        'ftp.ncbi.nlm.nih.gov::genomes/genbank/bacteria/'+path,
                        'scratch/'+organism])