Mercurial > repos > matt-shirley > sra_tools

changeset 12:b77840618b8f draft

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debugging SRA datatype
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 16:05:30 -0400
parents cdba74ec9eca
children 45031bbf6b27
files sra.py
diffstat 1 files changed, 5 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/sra.py	Mon Jun 17 14:26:40 2013 -0400
+++ b/sra.py	Mon Jun 17 16:05:30 2013 -0400
@@ -2,17 +2,11 @@
 Sra class
 """
 
-import galaxy.datatypes.binary
+import binascii
 from galaxy.datatypes.binary import Binary
-import data, logging, binascii
+from galaxy.datatypes.data import Data
 from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes import metadata
 from galaxy.datatypes.sniff import *
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( 'bx-python' )
-import os, subprocess, tempfile
-import struct
 
 class Sra( Binary ):
     """ Sequence Read Archive (SRA) """
@@ -28,12 +22,13 @@
             header = open(filename).read(8)
             if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
                 return True
-            return False
+            else:
+                return False
         except:
             return False
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
-            dataset.peek  = 'Binary sra file'
+            dataset.peek  = 'Binary SRA file'
             dataset.blurb = data.nice_size(dataset.get_size())
         else:
             dataset.peek = 'file does not exist'
@@ -43,5 +38,3 @@
             return dataset.peek
         except:
             return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
-
-Binary.register_sniffable_binary_format('sra', 'sra', Sra)