# HG changeset patch
# User Matthew Shirley <mdshw5@gmail.com>
# Date 1352912838 18000
# Node ID be22544bfafa071cfb4adf5df28382400ecf4970
# Parent  aa7ab53c53bfeb9239c8964546165654f3d805fa
First version of the python script that may work. Whole tool is still not functional.

diff -r aa7ab53c53bf -r be22544bfafa sra_fetch.py
--- a/sra_fetch.py	Tue Nov 13 22:32:13 2012 -0500
+++ b/sra_fetch.py	Wed Nov 14 12:07:18 2012 -0500
@@ -1,5 +1,5 @@
 from ftplib import FTP
-import os, sys, os.path
+import sys
 
 # Get accession number from argument
 accession = sys.argv[1]
@@ -7,10 +7,14 @@
 middle = accession[3:5]
 suffix = accession[6:8]
 
+# NCBI SRA FTP site
 ftp = FTP('ftp.ncbi.nlm.nih.gov')
 
-def handleDownload(block):
-    file.write(block)
-    
+# Open stdout and transfer requested SRA as a file
 ftp.login()
-ftp.cwd('/sra/sra-instant/reads/BySample/sra/
+ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' + 
+        prefix + '/' +
+        prefix + middle + '/' +
+        prefix + middle + suffix + '/' +
+        prefix + middle + suffix + '.sra', sys.stdout)
+ftp.quit()