# HG changeset patch
# User Matthew Shirley <mdshw5@gmail.com>
# Date 1352918144 18000
# Node ID f74bbb22bf621601d0e33f783d9896c19a4792b3
# Parent  8ce70ee5f33570504a85ea9078483008228a3af8
Fixed typos in python script.

diff -r 8ce70ee5f335 -r f74bbb22bf62 sra_fetch.py
--- a/sra_fetch.py	Wed Nov 14 13:13:32 2012 -0500
+++ b/sra_fetch.py	Wed Nov 14 13:35:44 2012 -0500
@@ -3,6 +3,7 @@
 
 # Get accession number from argument
 accession = sys.argv[1]
+outfile = sys.argv[2]
 prefix = accession[0:3]
 middle = accession[3:6]
 suffix = accession[6:9]
@@ -10,12 +11,13 @@
 # NCBI SRA FTP site
 ftp = FTP('ftp-trace.ncbi.nih.gov')
 
-# Open stdout and transfer requested SRA as a file
-ftp.login()
+# Open file and transfer requested SRA as a file
+sra = open(outfile, 'wb')
+ftp.login('ftp')
 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.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
 ftp.quit()