src/obiconvert.py

@@ -33,6 +33,7 @@ from obitools.options import getOptionManager
 from obitools.format.options import addInOutputOption, sequenceWriterGenerator
 from obitools.ecopcr.options import addTaxonomyDBOptions
 
+from sys import stderr
 
 if __name__ == '__main__':
     
@@ -42,4 +43,12 @@ if __name__ == '__main__':
     writer = sequenceWriterGenerator(options)
        
     for entry in entries:
-        writer(entry)
+        if options.skiperror:
+            try:
+                writer(entry)
+            except:
+                print >>stderr,"Skip writing of sequence : %s" % entry.id
+        else:
+            writer(entry)
+            
+