+ changed python and c code in order to perform easier parameter handling and
[qpalma.git] / tests / test_qpalma_prediction.py
index 936a163..8e5e37a 100644 (file)
@@ -98,7 +98,6 @@ class TestQPalmaPrediction(unittest.TestCase):
             print 'size'
             print len(example)
 
-
       # fetch the data needed
       g_dir    = run['dna_flat_files'] #'/fml/ag-raetsch/share/projects/genomes/A_thaliana_best/genome/'
       acc_dir  = '/fml/ag-raetsch/home/fabio/tmp/interval_query_files/acc'
@@ -112,11 +111,10 @@ class TestQPalmaPrediction(unittest.TestCase):
       accessWrapper = DataAccessWrapper(g_dir,acc_dir,don_dir,g_fmt,s_fmt)
       seqInfo = SeqSpliceInfo(accessWrapper,range(1,num_chromo))
 
-
-
       qp = QPalma(True)
       #qp.init_prediction(run,set_name)
       allPredictions = qp.predict(run,self.prediction_set,param,seqInfo )
+
       for current_prediction in allPredictions:
          align_str = print_prediction(current_prediction)
          print align_str
@@ -134,6 +132,7 @@ class TestQPalmaPrediction(unittest.TestCase):
          print alignment_reconstruct(current_prediction,numExons)
          #print id,start_pos,predExons
 
+      print 'Problem counter is %d' % qp.problem_ctr 
 
 if __name__ == '__main__':
    suite = unittest.TestLoader().loadTestsFromTestCase(TestQPalmaPrediction)