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comparison sra_fetch.py @ 3:01dec8611542 draft

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Python script successfully returns SRA archive from accession.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:05:14 -0500
parents be22544bfafa
children f74bbb22bf62
comparison
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2:be22544bfafa 3:01dec8611542
1 from ftplib import FTP 1 from ftplib import FTP
2 import sys 2 import sys
3 3
4 # Get accession number from argument 4 # Get accession number from argument
5 accession = sys.argv[1] 5 accession = sys.argv[1]
6 prefix = accession[0:2].uppercase() 6 prefix = accession[0:3]
7 middle = accession[3:5] 7 middle = accession[3:6]
8 suffix = accession[6:8] 8 suffix = accession[6:9]
9 9
10 # NCBI SRA FTP site 10 # NCBI SRA FTP site
11 ftp = FTP('ftp.ncbi.nlm.nih.gov') 11 ftp = FTP('ftp-trace.ncbi.nih.gov')
12 12
13 # Open stdout and transfer requested SRA as a file 13 # Open stdout and transfer requested SRA as a file
14 ftp.login() 14 ftp.login()
15 ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' + 15 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' +
16 prefix + '/' + 16 prefix + '/' +
17 prefix + middle + '/' + 17 prefix + middle + '/' +
18 prefix + middle + suffix + '/' + 18 prefix + middle + suffix + '/')
19 prefix + middle + suffix + '.sra', sys.stdout) 19 ftp.pwd()
20 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sys.stdout)
20 ftp.quit() 21 ftp.quit()