obi import: added basic taxdump import

python/obitools3/commands/import.pyx

@@ -8,6 +8,8 @@ from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column
 from obitools3.dms.obiseq cimport Nuc_Seq
 from obitools3.dms import DMS
+from obitools3.dms.taxo.taxo cimport Taxonomy
+
 
 from obitools3.utils cimport tobytes, \
                              get_obitype, \
@@ -19,7 +21,10 @@ from obitools3.dms.capi.obitypes cimport obitype_t, \
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
-from obitools3.apps.optiongroups import addSequenceInputOption, addTabularInputOption, addMinimalOutputOption
+from obitools3.apps.optiongroups import addSequenceInputOption, \
+                                        addTabularInputOption, \
+                                        addMinimalOutputOption, \
+                                        addTaxdumpInputOption
 
 from obitools3.uri.decode import open_uri
 
@@ -42,7 +47,7 @@ def addOptions(parser):
     addSequenceInputOption(parser)
     addTabularInputOption(parser)
     addMinimalOutputOption(parser)
-#    addTaxdumpInputOption(parser)
+    addTaxdumpInputOption(parser)
 
 
 def run(config):
@@ -85,6 +90,19 @@ def run(config):
     logger("info","obi import : imports file into an DMS")
     
     input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not open input URI")
+
+    # TODO read taxdump with URI?
+    if 'taxdump' in config['obi']:
+        taxo = Taxonomy.open_taxdump(input[0], config['obi']['taxdump'])
+        # Read prefix (temporary fix)
+        uri = config['obi']['outputURI'].split('/')
+        idx = uri.index('taxonomy') + 1
+        taxo.write(uri[idx])
+        taxo.close()
+        input[0].close()
+        return
         
     if input[2]==Nuc_Seq:
         v = View_NUC_SEQS