Throw a warning instead of an exception when a GFF target feature doe…

…s not exist

README.md

@@ -87,6 +87,9 @@ $ chakin feature load_fasta \
 
 ## History
 
+- 2.2.3
+    - Throw a warning instead of an exception when a GFF target feature does not exist
+
 - 2.2.2
     - Bug fixes and improvements to the expression module
 

chado/feature/__init__.py

@@ -1139,7 +1139,8 @@ def _add_target(self, feat, target_str):
 
         target = target_str.split(' ')
         if len(target) != 3 and len(target) != 4:
-            raise Exception('Malformed Target value: {}'.format(target_str))
+            warn('Malformed Target value: {}, skipping'.format(target_str))
+            return
 
         strand = 1
         if len(target) == 4:
@@ -1148,7 +1149,8 @@ def _add_target(self, feat, target_str):
             elif target[3] == '-':
                 strand = -1
             else:
-                raise Exception('Malformed Target value (bad strand): {}'.format(target_str))
+                warn('Malformed Target value (bad strand): {}, skipping'.format(target_str))
+                return
 
         landmark_str = target[0]
         landmark = None
@@ -1164,7 +1166,8 @@ def _add_target(self, feat, target_str):
                 break
 
         if landmark is None:
-            raise Exception('Malformed Target value (unknown target): {}'.format(target_str))
+            warn('Malformed Target value (unknown target): {}, skipping'.format(target_str))
+            return
 
         self._do_add_featureloc(landmark, feat, rank, start, end, strand)
 

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="chado",
-    version='2.2.2',
+    version='2.2.3',
     description="Chado library",
     author="Anthony Bretaudeau",
     author_email="[email protected]",