changeset 16:93a60318b9ca draft

updates to SRA datatype

--- a/sra.py	Mon Jun 17 17:08:53 2013 -0400
+++ b/sra.py	Mon Jun 17 20:30:16 2013 -0400
@@ -1,14 +1,16 @@
 """
 Sra class
 """
-
+import logging
 import binascii
-from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.data import Data
-from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.data import *
 from galaxy.datatypes.sniff import *
+from galaxy.datatypes.binary import *
+from galaxy.datatypes.metadata import *
 
-class Sra( Binary ):
+log = logging.getLogger(__name__)
+
+class SRA( Binary ):
     """ Sequence Read Archive (SRA) """
     file_ext = 'sra'
 
@@ -37,4 +39,7 @@
         try:
             return dataset.peek
         except:
-            return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
+            return 'Binary SRA file (%s)' % ( data.nice_size(dataset.get_size()))
+
+if hasattr(Binary, 'register_sniffable_binary_format'):
+    Binary.register_sniffable_binary_format('SRA', 'SRA', SRA)

--- a/sra_fetch.py	Mon Jun 17 17:08:53 2013 -0400
+++ b/sra_fetch.py	Mon Jun 17 20:30:16 2013 -0400
@@ -15,7 +15,6 @@
     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:
@@ -56,7 +55,6 @@
         ## 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