obi import: added an option to specify the NA value in the input file

(default is 'NA', same as in R's read.table function)

python/obitools3/commands/import.pyx

@@ -104,9 +104,15 @@ def addOptions(parser):
                      const='pep',
                      help="Input file contains protein sequences")
 
+    group.add_argument('--NA',
+                     action="store", dest="import:NA",
+                     metavar='<NA_value>',
+                     default='NA',
+                     type=str,
+                     help="Character string for Not Available values in the input file "
+                          "(default: 'NA'")
+
 
-# TODO: Handling of NA values. Check None. Specify in doc? None or NA? Possiblity to specify in option?
-# look in R read.table option to specify NA value
 def run(config):
     
     cdef   int         i
@@ -192,6 +198,10 @@ def run(config):
                             
                 value = seq['tags'][tag]
                 
+                # Check NA value
+                if value == config['import']['NA'] :
+                    value = None
+                
                 if tag not in dcols :
                     
                     value_type = type(value)
@@ -209,7 +219,7 @@ def run(config):
                     
                     if value_obitype != OBI_VOID :
                         dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names), value_obitype)
-
+                                                
                         # Fill value
                         dcols[tag][0][i] = value