obi annotate: fixed a bug with --with-taxon-at-rank option and minor

improvements

python/obitools3/commands/annotate.pyx

@@ -13,9 +13,18 @@ from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
 import time
 import math 
 
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN
+
  
 __title__="Annotate views with new tags and edit existing annotations"
 
+
+SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
+
  
 def addOptions(parser):
     
@@ -152,7 +161,7 @@ def sequenceTaggerGenerator(config, taxo=None):
             toSet[i][j] = tobytes(toSet[i][j])
 
     annoteRank=[]
-    if 'taxon_at_rank' in config['annotate']:
+    if config['annotate']['taxon_at_rank']:
         if taxo is not None:
             annoteRank = config['annotate']['taxon_at_rank']
         else:
@@ -313,8 +322,9 @@ def run(config):
         keep = set(keep)
     
         if clear or keep:
-            for k in o_view.keys():
-                if k not in keep:
+            keys = [k for k in o_view.keys()]
+            for k in keys:
+                if k not in keep and k not in SPECIAL_COLUMNS:
                     o_view.delete_column(k)
         else:
             for k in toDelete: