Cython: added an option for input taxdump and and an option for the

maximum number of elements in columns with multiple elements per line

python/obitools3/apps/optiongroups/__init__.py

@@ -155,6 +155,14 @@ def __addTaxonomyInputOption(optionManager):
     
     #TODO option bool to download taxo if URI doesn't exist
 
+def __addTaxdumpInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for taxdump")
+
+    group.add_argument('--taxdump',
+                     action="store", dest="obi:taxdump",
+                     default=None,
+                     help="Taxdump path")
+
 def addMinimalInputOption(optionManager):
     __addInputOption(optionManager)
     
@@ -169,12 +177,15 @@ def addTabularInputOption(optionManager):
 def addTaxonomyInputOption(optionManager):
     __addTaxonomyInputOption(optionManager)
 
+def addTaxdumpInputOption(optionManager):
+    __addTaxdumpInputOption(optionManager)
+
 def addAllInputOption(optionManager):
     __addInputOption(optionManager)
     __addSequenceInputOption(optionManager)
     __addTabularInputOption(optionManager)
     __addTaxonomyInputOption(optionManager)
-    
+    __addTaxdumpInputOption(optionManager)    
     
 def __addOutputOption(optionManager):
     
@@ -190,6 +201,16 @@ def __addOutputOption(optionManager):
                  default=False,
                  help="Don't create an output DMS is it is not existing")
 
+    group.add_argument('--max-elts',
+                 action="store", dest="obi:maxelts",
+                 metavar='<N>',
+                 default=1000,
+                 type=int,
+                 help="Maximum number of elements per line in a column "
+                      "(e.g. the number of different keys in a dictionary-type "
+                      "key from sequence headers). If the number of different keys "
+                      "is greater than N, the values are stored as character strings")
+
 
 def addMinimalOutputOption(optionManager):
     __addOutputOption(optionManager)