domain annotation is now sorted by sequence-id and sequence-start for simple architecture output

scripts/simple_arch.py

@@ -147,10 +147,9 @@ def main():
             taxid2name[taxid] = name
 
     with open(finalPredictionsFile,'w') as outFile:
-        for query in objReturn:
-            for i in range(0,len(objReturn[query])):
-                if not objReturn[query][i] is None:
-                    data     = objReturn[query][i]
+        for query in sorted(objReturn.keys()):
+            sortedHits = sorted( (data for data in objReturn[query] if data is not None), key=lambda d:d[SEQ_START] )
+            for data in sortedHits:
                 evalue   = data[I_EVALUE]
                 bitscore = data[SCORE]
                 modid    = data[MODEL_NAME]