Mercurial > repos > matt-shirley > sra_fetch

changeset 5:f74bbb22bf62 draft

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Fixed typos in python script.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:35:44 -0500
parents 8ce70ee5f335
children 20a054a7e2fd
files sra_fetch.py
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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()