Checks for very old format of seeds

python/orgasm/__init__.py

@@ -15,10 +15,37 @@ def getOutput(config):
     @param config: a configuration object
     @return: the path for the output files
     '''
+    logger = config['orgasm']['logger']
     
     dirname = "%s.oas" % config['orgasm']['outputfilename']
     if not os.path.exists(dirname):
-        os.makedirs(dirname) 
+        if os.path.exists('%s.oax' % config['orgasm']['outputfilename']):
+            
+            if config['buildgraph']['reformat']:
+                #
+                # Reformating outpout according to the new format
+                #
+                os.makedirs(dirname) 
+                for extension in ['oax','omx','gml','stats',
+                                  'intermediate.gml','.intermediate.oax']:
+                    if os.path.exists('%s.%s' % (config['orgasm']['outputfilename'],
+                                                 extension)):
+                        os.renames('%s.%s' % (config['orgasm']['outputfilename'],
+                                              extension), 
+                                   '%s.oas/assembling.%s' % (config['orgasm']['outputfilename'],
+                                                             extension))
+                sys.exit(0)
+            else:
+                #
+                # Exit with an error because the format is obsolete.
+                #
+                logger.error("The %s assembly is not stored according to new format" % config['orgasm']['outputfilename'])
+                logger.error('Run the oa buildgraph command with the --reformat option')
+                sys.exit(1)
+        else:
+            os.makedirs(dirname)
+            
+            
         
     return "%s/assembling" % dirname
     
@@ -120,7 +147,7 @@ def getSeeds(index,config):
     forceseeds=config['buildgraph']['forceseeds']
     
 
-    filename="%s.oas/assembling.omx"
+    filename="%s.oas/assembling.omx" % output
     
     #
     # Check if the seeds are not correctly placed in the oas directory
@@ -154,6 +181,13 @@ def getSeeds(index,config):
                 probes = pickle.load(fseeds)
             logger.info("Load matches from previous run : %d probe sets restored" % len(probes))
     
+            if not isinstance(list(probes.values())[0][0], dict):
+                logger.error("Too old version of probes matches that cannot be reformated")
+                logger.error("Generate a new probe match set using the command oa seeds --seeds command")
+                logger.error("The old unsuable seed match has been erased")
+                os.remove(filename)
+                sys.exit(1)
+                
             oldversion=False
             for probename in probes:
                 s = probes[probename][1]