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comparison sra_fetch.py @ 5:f74bbb22bf62 draft

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Fixed typos in python script.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:35:44 -0500
parents 01dec8611542
children d7708f338c82
comparison
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4:8ce70ee5f335 5:f74bbb22bf62
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 outfile = sys.argv[2]
6 prefix = accession[0:3] 7 prefix = accession[0:3]
7 middle = accession[3:6] 8 middle = accession[3:6]
8 suffix = accession[6:9] 9 suffix = accession[6:9]
9 10
10 # NCBI SRA FTP site 11 # NCBI SRA FTP site
11 ftp = FTP('ftp-trace.ncbi.nih.gov') 12 ftp = FTP('ftp-trace.ncbi.nih.gov')
12 13
13 # Open stdout and transfer requested SRA as a file 14 # Open file and transfer requested SRA as a file
14 ftp.login() 15 sra = open(outfile, 'wb')
16 ftp.login('ftp')
15 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' + 17 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' +
16 prefix + '/' + 18 prefix + '/' +
17 prefix + middle + '/' + 19 prefix + middle + '/' +
18 prefix + middle + suffix + '/') 20 prefix + middle + suffix + '/')
19 ftp.pwd() 21 ftp.pwd()
20 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sys.stdout) 22 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
21 ftp.quit() 23 ftp.quit()