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comparison sra_fetch.py @ 2:be22544bfafa draft

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First version of the python script that may work. Whole tool is still not functional.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 12:07:18 -0500
parents aa7ab53c53bf
children 01dec8611542
comparison
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1:aa7ab53c53bf 2:be22544bfafa
1 from ftplib import FTP 1 from ftplib import FTP
2 import os, sys, os.path 2 import sys
3 3
4 # Get accession number from argument 4 # Get accession number from argument
5 accession = sys.argv[1] 5 accession = sys.argv[1]
6 prefix = accession[0:2].uppercase() 6 prefix = accession[0:2].uppercase()
7 middle = accession[3:5] 7 middle = accession[3:5]
8 suffix = accession[6:8] 8 suffix = accession[6:8]
9 9
10 # NCBI SRA FTP site
10 ftp = FTP('ftp.ncbi.nlm.nih.gov') 11 ftp = FTP('ftp.ncbi.nlm.nih.gov')
11 12
12 def handleDownload(block): 13 # Open stdout and transfer requested SRA as a file
13 file.write(block)
14
15 ftp.login() 14 ftp.login()
16 ftp.cwd('/sra/sra-instant/reads/BySample/sra/ 15 ftp.retrbinary('/sra/sra-instant/reads/ByRun/sra/' +
16 prefix + '/' +
17 prefix + middle + '/' +
18 prefix + middle + suffix + '/' +
19 prefix + middle + suffix + '.sra', sys.stdout)
20 ftp.quit()