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changeset 3:01dec8611542 draft

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Python script successfully returns SRA archive from accession.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:05:14 -0500
parents be22544bfafa
children 8ce70ee5f335
files sra_fetch.py
diffstat 1 files changed, 8 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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()