import subprocess, os
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:
    latest = os.path.join(organism, "latest_assembly_versions")
    for path in ftp.nlst(latest):
        accession = path.split("/")[-1]
        fasta = accession+"_genomic.fna.gz"
        subprocess.call(['rsync',
                         '--recursive',
                         '-vv',
                         '--copy-links',
                         '--dry-run',
                         '-f=+ '+fasta,
                         #'-f=- *',
                         'ftp.ncbi.nlm.nih.gov::genomes/genbank/bacteria/'+latest,
                         '--log-file=scratch/test_dir/log.txt',
                         'scratch/' + organism])