Quality columns are now optional in NUC_SEQS views + minor fixes

python/obitools3/commands/import.pyx

@@ -42,8 +42,6 @@ def addOptions(parser):
                      type=str,
                      required=True,
                      help="Name of the default DMS for reading and writing data")
-
-    group=parser.add_argument_group('obi import specific options')
     
     group.add_argument('--skip',
                      action="store", dest="import:skip",
@@ -88,10 +86,11 @@ def addOptions(parser):
                      const='pep',
                      help="Input file contains protein sequences")
 
-    
-    
+
+
+# TODO: Handling of NA values
 def run(config):
-    pb = ProgressBar(35000000,config,seconde=5)
+    #pb = ProgressBar(35000000, config, seconde=5)
       
     inputs = uopen(config['import']['filename'])
     
@@ -105,35 +104,28 @@ def run(config):
         get_quality = True
     else:
         raise RuntimeError('No file format specified')
-    
-    # Temporary way to handle NA values
-    #NA_list = ["nan"]
-    
+        
     # Create DMS
     d = OBIDMS(config['obi']['defaultdms'])
     
     # Create view
-    view = d.new_view(config['import']['destview'], view_type=view_type)
+    view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
     
     i = 0
     for seq in iseq:
-        pb(i)
+        #pb(i)
         view[i].set_id(seq['id'])
         view[i].set_definition(seq['definition'])
         view[i].set_sequence(seq['sequence'])
         if get_quality :
             view[i].set_quality(seq['quality'])
         for tag in seq['tags'] :
-            #print(tag, seq['tags'][tag])
-            #if seq['tags'][tag] not in NA_list :
             view[i][tag] = seq['tags'][tag]
         i+=1
 
-    #print(i)
     print(view.__repr__())
 
-    view.save_and_close()
+    view.save_and_close()    
     d.close()
     
     print("Done.")
-