Mercurial > repos > matt-shirley > sra_fetch
view sra_fetch.py @ 2:be22544bfafa draft
First version of the python script that may work. Whole tool is still not functional.
author | Matthew Shirley <mdshw5@gmail.com> |
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date | Wed, 14 Nov 2012 12:07:18 -0500 |
parents | aa7ab53c53bf |
children | 01dec8611542 |
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from ftplib import FTP import sys # Get accession number from argument accession = sys.argv[1] prefix = accession[0:2].uppercase() middle = accession[3:5] suffix = accession[6:8] # NCBI SRA FTP site ftp = FTP('ftp.ncbi.nlm.nih.gov') # Open stdout and transfer requested SRA as a file ftp.login() ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' + prefix + '/' + prefix + middle + '/' + prefix + middle + suffix + '/' + prefix + middle + suffix + '.sra', sys.stdout) ftp.quit()