obi import: fixed creation of quality columns (to discuss)

python/obitools3/commands/import.pyx

@@ -19,7 +19,8 @@ from obitools3.utils cimport tobytes, \
                              update_obitype
 
 from obitools3.dms.capi.obitypes cimport obitype_t, \
-                                         OBI_VOID
+                                         OBI_VOID, \
+                                         OBI_QUAL
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
@@ -45,7 +46,7 @@ def addOptions(parser):
     
     addSequenceInputOption(parser)
     addMinimalOutputOption(parser)
-
+#    addTaxdumpInputOption(parser)
 
 
 def run(config):
@@ -89,6 +90,8 @@ def run(config):
     
     input = open_uri(config['obi']['inputURI'])
     
+    print(input)
+    
     if input[2]==Nuc_Seq:
         v = View_NUC_SEQS
     else:
@@ -97,9 +100,13 @@ def run(config):
     output = open_uri(config['obi']['outputURI'],
                       input=False,
                       newviewtype=v)
+                      #quality=get_quality)  # TODO
 
-    #print(input)
-    #print(output)
+    if output is None:
+        raise Exception("Could not create output view")
+
+    print("input:", input)
+    print("output:", output)
         
     pb = ProgressBar(1000000, config, seconde=5)   # TODO should be number of records in file
     
@@ -107,14 +114,11 @@ def run(config):
     
     NA_value = config['obi']['nastring']
     
-    get_quality = False
     NUC_SEQS_view = False
     if isinstance(output[1], View) :
         view = output[1]
         if output[2] == View_NUC_SEQS :
             NUC_SEQS_view = True
-            if "QUALITY" in view :      # TODO
-                get_quality = True
     else: 
         raise NotImplementedError()
     
@@ -123,8 +127,6 @@ def run(config):
         id_col = view[b"ID"]
         def_col = view[b"DEFINITION"]
         seq_col = view[b"NUC_SEQ"]
-        if get_quality :
-            qual_col = view[b"QUALITY"]
      
     dcols = {}
      
@@ -134,6 +136,15 @@ def run(config):
         pb(i)
                 
         if NUC_SEQS_view :
+            
+            # Check if there is a sequencing quality associated     # TODO
+            if i == 0:
+                get_quality = b"QUALITY" in seq
+                if get_quality:
+                    print("yah")
+                    Column.new_column(view, b"QUALITY", OBI_QUAL)
+                    qual_col = view[b"QUALITY"]
+            
             id_col[i] = seq.id
             def_col[i] = seq.definition
             seq_col[i] = seq.seq