Mercurial > repos > matt-shirley > sra_fetch
view sra_fetch.py @ 4:8ce70ee5f335 draft
Updated wrapper script. First version that should work properly.
author | Matthew Shirley <mdshw5@gmail.com> |
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date | Wed, 14 Nov 2012 13:13:32 -0500 |
parents | 01dec8611542 |
children | f74bbb22bf62 |
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from ftplib import FTP import sys # Get accession number from argument accession = sys.argv[1] prefix = accession[0:3] middle = accession[3:6] suffix = accession[6:9] # NCBI SRA FTP site ftp = FTP('ftp-trace.ncbi.nih.gov') # Open stdout and transfer requested SRA as a file ftp.login() ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' + prefix + '/' + prefix + middle + '/' + prefix + middle + suffix + '/') ftp.pwd() ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sys.stdout) ftp.quit()