Mercurial > repos > matt-shirley > sra_fetch

comparison sra_fetch.py @ 9:cf0980cfd040 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author matt-shirley
date Tue, 27 Nov 2012 13:38:35 -0500
parents 61d634d123c0
children
comparison
equal deleted inserted replaced
8:61d634d123c0 9:cf0980cfd040
1 from ftplib import FTP
2 import sys
3
4 # Get accession number from argument
5 accession = sys.argv[1]
6 outfile = sys.argv[2]
7 prefix = accession[0:3]
8 middle = accession[3:6]
9 suffix = accession[6:9]
10
11 # NCBI SRA FTP site
12 ftp = FTP('ftp-trace.ncbi.nih.gov')
13
14 # Open file and transfer requested SRA as a file
15 # Try to change the working directory until it works
16 sra = open(outfile, 'wb')
17 ftp.login('ftp')
18 connected = False
19 while not connected:
20 try:
21 ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' +
22 prefix + '/' +
23 prefix + middle + '/' +
24 prefix + middle + suffix + '/')
25 connected = True
26 except:
27 pass
28
29 ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
30 ftp.quit()