SHOW:
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- or go back to the newest paste.
| 1 | - | import subprocess |
| 1 | + | import subprocess, os |
| 2 | from ftplib import FTP | |
| 3 | ||
| 4 | ftp_site = 'ftp.ncbi.nlm.nih.gov' | |
| 5 | ftp = FTP(ftp_site) | |
| 6 | ftp.login() | |
| 7 | ftp.cwd('genomes/genbank/bacteria')
| |
| 8 | dirs = ftp.nlst() | |
| 9 | for organism in dirs: | |
| 10 | latest = os.path.join(organism, "latest_assembly_versions") | |
| 11 | for path in ftp.nlst(latest): | |
| 12 | - | for path in ftp.nlst(organism+"/latest_assembly_versions"): |
| 12 | + | |
| 13 | fasta = accession+"_genomic.fna.gz" | |
| 14 | subprocess.call(['rsync', | |
| 15 | - | #print(path) |
| 15 | + | '--recursive', |
| 16 | - | #print(accession) |
| 16 | + | '-vv', |
| 17 | - | #print(fasta) |
| 17 | + | '--copy-links', |
| 18 | '--dry-run', | |
| 19 | - | # path is symbolically link at genomes/genbank/bacteria/organism |
| 19 | + | '-f=+ '+fasta, |
| 20 | - | '--recursive', |
| 20 | + | #'-f=- *', |
| 21 | - | '--copy-links', |
| 21 | + | 'ftp.ncbi.nlm.nih.gov::genomes/genbank/bacteria/'+latest, |
| 22 | - | '--dry-run', |
| 22 | + | '--log-file=scratch/test_dir/log.txt', |
| 23 | - | '--include='+fasta, |
| 23 | + | 'scratch/' + organism]) |
