Add management of quality scores

src/obitools/__init__.py

@@ -474,6 +474,9 @@ class SubSequence(WrappedBioSequence):
         self._info['cut']='[%d,%d,%s]' % self._indices
         self._eval['cut']=True
         
+        if hasattr(reference,'quality'):
+            self.quality = reference.quality[self._location]
+        
     def getId(self):
         d = self._id or ("%s_SUB" % self.wrapped.id)
         return d
@@ -523,6 +526,9 @@ class DNAComplementSequence(WrappedBioSequence):
         assert reference.isNucleotide()
         self._info['complemented']=True
         self._eval['complemented']=True
+        if hasattr(reference,'quality'):
+            self.quality = reference.quality[::-1]
+
            
     def getId(self):
         d = self._id or ("%s_CMP" % self.wrapped.id)