blanchette run ready

src/parse_sequences.py

@@ -48,6 +48,7 @@ def run_fasta(input, modules_to_parse,dataset,ss = "",arguments={}):
         with open(input, "rU") as f:
             for num,record in enumerate(SeqIO.parse(f, "fasta")):
                 id = record.id
+                seq = record.seq
                 prediction_scores[id] = {}
                 if "T" in seq:
                     seq = str(record.seq).replace("T","U")
@@ -62,7 +63,7 @@ def run_fasta(input, modules_to_parse,dataset,ss = "",arguments={}):
                         prediction_scores[id][modules_to_parse[ind]] = (maxs[ind][0], maxs[ind][1])
                     else:
                         prediction_scores[id][modules_to_parse[ind]] = (0, [])
-        pickle.dump(prediction_scores, open("prediction_test.cPickle", "wb"))
+        pickle.dump(prediction_scores, open("prediction_ircm.cPickle", "wb"))
     else:
         if "T" in input:
             input = str(input).replace("T","U")