Mercurial > repos > matt-shirley > sra_fetch

changeset 1:aa7ab53c53bf draft

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Started working on the python FTP script.
author matt-shirley
date Tue, 13 Nov 2012 22:32:13 -0500
parents abdb4762ebcb
children be22544bfafa
files sra_fetch.py
diffstat 1 files changed, 16 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sra_fetch.py	Tue Nov 13 22:32:13 2012 -0500
@@ -0,0 +1,16 @@
+from ftplib import FTP
+import os, sys, os.path
+
+# Get accession number from argument
+accession = sys.argv[1]
+prefix = accession[0:2].uppercase()
+middle = accession[3:5]
+suffix = accession[6:8]
+
+ftp = FTP('ftp.ncbi.nlm.nih.gov')
+
+def handleDownload(block):
+    file.write(block)
+    
+ftp.login()
+ftp.cwd('/sra/sra-instant/reads/BySample/sra/