changeset 14:082fd6374582 draft

fallback to getopt for fetch_sra.py

--- a/sra_fetch.py	Mon Jun 17 16:17:33 2013 -0400
+++ b/sra_fetch.py	Mon Jun 17 17:07:57 2013 -0400
@@ -1,19 +1,24 @@
 import sys
 import os
 from ftplib import FTP
-import argparse
+try:
+    import argparse
+except ImportError:
+    import getopt
 
 def main(args):
     """ Get accession number from argument """
-    prefix = args.accession[0:3]
-    middle = args.accession[3:6]
-    suffix = args.accession[6:9]
+    if module_exists('argparse'):
+        args = dict(vars(args))
+    prefix = args['accession'][0:3]
+    middle = args['accession'][3:6]
+    suffix = args['accession'][6:9]
 
     ftp = FTP('ftp-trace.ncbi.nih.gov')
-
+    print args
     # Open file and transfer requested SRA as a file
     # Try to change the working directory until it works
-    with open(args.out, 'wb') as sra:
+    with open(args['out'], 'wb') as sra:
         ftpPath = os.path.join('/sra/sra-instant/reads/ByRun/sra/',
                                prefix,
                                prefix + middle,
@@ -29,13 +34,33 @@
         ftp.retrbinary('RETR ' + prefix + middle + suffix + '.sra', sra.write)
         ftp.quit()
 
+def module_exists(module_name):
+    try:
+        __import__(module_name)
+    except ImportError:
+        return False
+    else:
+        return True
+
 def arguments():
     parser = argparse.ArgumentParser(description="Download an SRA from the NCBI SRA FTP")
-    parser.add_argument('accession', type=str, help="SRA accession ex: SRR000001")
+    parser.add_argument('-a', '--accession', type=str, help="SRA accession ex: SRR000001")
     parser.add_argument('-o', '--out', type=str, help="Name for SRA file ")
     args = parser.parse_args()
     return args
 
 if __name__ == "__main__":
-    args = arguments()
+    if module_exists('argparse'):
+        args = arguments()
+    else:
+        ## fall back to getopt for python < 2.7
+        args = dict()
+        options, remainder = getopt.getopt(sys.argv[1:], 'a:o:', ['accession=', 'out='])
+        print options
+        for opt, arg in options:
+            if opt in ('-a', '--accession'):
+                args['accession'] = arg
+            elif opt in ('-o', '--out'):
+                args['out'] = arg
+
     main(args)