Testing

modules/bindings/pymod/hhblits.py

@@ -577,13 +577,17 @@ class HHblits:
         job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
                                env=env, stdout=subprocess.PIPE,
                                stderr=subprocess.PIPE)
-        sout, _ = job.communicate()
+        sout, serr = job.communicate()
         lines = sout.splitlines()
         for line in lines:
             if 'error' in line.lower():
                 ost.LogWarning('Predicting secondary structure for MSA '+
                                '(%s) failed, on command: %s' % (a3m_file, line))
             return a3m_file
+            print "BIENCHEN", line
+        lines = serr.splitlines()
+        for line in lines:
+            print "BIENCHEN", line
         return a3m_file
 
     def A3MToProfile(self, a3m_file, hhm_file=None):

modules/bindings/tests/test_hhblits.py

@@ -115,16 +115,6 @@ class TestHHblitsBindings(unittest.TestCase):
                                        'TSKYR')
         self.hh = hhblits.HHblits(query_seq, self.hhroot)
         a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/hhblitsdb')
-        print "A3M"
-        with open(a3m) as fh:
-            for line in fh:
-                line = line.strip()
-                print line
-        print "TESTFILE"
-        with open("testfiles/testali.a3m") as fh:
-            for line in fh:
-                line = line.strip()
-                print line
         self.assertTrue(filecmp.cmp(a3m, "testfiles/testali.a3m"))
 
     def testA3mToProfileFileName(self):