# HG changeset patch
# User Matthew Shirley <mdshw5@gmail.com>
# Date 1352916314 18000
# Node ID 01dec86115428450dfd1c1e5c633aa911018a36d
# Parent  be22544bfafa071cfb4adf5df28382400ecf4970
Python script successfully returns SRA archive from accession.

diff -r be22544bfafa -r 01dec8611542 sra_fetch.py
--- a/sra_fetch.py	Wed Nov 14 12:07:18 2012 -0500
+++ b/sra_fetch.py	Wed Nov 14 13:05:14 2012 -0500
@@ -3,18 +3,19 @@
 
 # Get accession number from argument
 accession = sys.argv[1]
-prefix = accession[0:2].uppercase()
-middle = accession[3:5]
-suffix = accession[6:8]
+prefix = accession[0:3]
+middle = accession[3:6]
+suffix = accession[6:9]
 
 # NCBI SRA FTP site
-ftp = FTP('ftp.ncbi.nlm.nih.gov')
+ftp = FTP('ftp-trace.ncbi.nih.gov')
 
 # Open stdout and transfer requested SRA as a file
 ftp.login()
-ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' + 
+ftp.cwd('/sra/sra-instant/reads/ByRun/sra/' + 
         prefix + '/' +
         prefix + middle + '/' +
-        prefix + middle + suffix + '/' +
-        prefix + middle + suffix + '.sra', sys.stdout)
+        prefix + middle + suffix + '/')
+ftp.pwd()
+ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sys.stdout)
 ftp.quit()