dummy commit 4

see previous commits...

modules/bindings/tests/test_hhblits.py

@@ -12,6 +12,7 @@ import datetime
 import ost
 from ost import seq
 from ost import settings
+from ost import io
 from ost.bindings import hhblits3
 
 class _UnitTestHHblitsLog(ost.LogSink):
@@ -154,14 +155,39 @@ class TestHHblitsBindings(unittest.TestCase):
         with open(hhfile) as tfh:
           tlst = tfh.readlines()
         with open("testfiles/test.hmm") as efh:
-          elst_1 = efh.readlines()
-        with open("testfiles/test_2.hmm") as efh:
-          elst_2 = efh.readlines()
-        assert(len(elst_1)==len(elst_2))
-        self.assertEqual(len(elst_1), len(tlst))
-        for i in range(0, len(elst_1)):
-            if not elst_1[i].startswith(('FILE', 'COM', 'DATE')):
-                self.assertTrue(elst_1[i] == tlst[i] or elst_2[i] == tlst[i])
+          elst = efh.readlines()
+        self.assertEqual(len(elst), len(tlst))
+        for i in range(0, len(elst)):
+            if elst[i].startswith("NULL"):
+                break # only compare header, profile is checked separately
+            if not elst[i].startswith(('FILE', 'COM', 'DATE')):
+                self.assertEqual(elst[i], tlst[i])
+
+        prof = io.LoadSequenceProfile(hhfile, format="hhm")
+        ref_prof = io.LoadSequenceProfile("testfiles/test.hmm", format="hhm")
+
+        hmm_transitions = [seq.HMMTransition.HMM_M2M, seq.HMMTransition.HMM_M2I,
+                           seq.HMMTransition.HMM_M2D, seq.HMMTransition.HMM_I2M,
+                           seq.HMMTransition.HMM_I2I, seq.HMMTransition.HMM_D2M,
+                           seq.HMMTransition.HMM_D2D]
+        self.assertEqual(prof.sequence, ref_prof.sequence)
+        self.assertEqual(prof.neff, ref_prof.neff)
+
+        for col, ref_col in zip(prof.columns, ref_prof.columns):
+            hmm_data = col.hmm_data
+            ref_hmm_data = ref_col.hmm_data
+            self.assertAlmostEqual(hmm_data.neff, ref_hmm_data.neff, places=2)
+            self.assertAlmostEqual(hmm_data.neff_i, ref_hmm_data.neff_i,
+                                   places=2)
+            self.assertAlmostEqual(hmm_data.neff_d, ref_hmm_data.neff_d,
+                                   places=2)
+            for t in hmm_transitions:
+                self.assertAlmostEqual(hmm_data.GetProb(t),
+                                       ref_hmm_data.GetProb(t), places=2)
+            for olc in "ARNDQEKSCMWYTVILGPHF":
+                self.assertAlmostEqual(col.GetFreq(olc), ref_col.GetFreq(olc),
+                                       places=2)
+
 
     def testA3mToProfileWithoutFileName(self):
         # test A3mToProfile to work without a given hhmake_file name
@@ -175,14 +201,38 @@ class TestHHblitsBindings(unittest.TestCase):
         with open(hhfile) as tfh:
           tlst = tfh.readlines()
         with open("testfiles/test.hmm") as efh:
-          elst_1 = efh.readlines()
-        with open("testfiles/test_2.hmm") as efh:
-          elst_2 = efh.readlines()
-        assert(len(elst_1)==len(elst_2))
-        self.assertEqual(len(elst_1), len(tlst))
-        for i in range(0, len(elst_1)):
-            if not elst_1[i].startswith(('FILE', 'COM', 'DATE')):
-                self.assertEqual(elst_2[i], tlst[i])
+          elst = efh.readlines()
+        self.assertEqual(len(elst), len(tlst))
+        for i in range(0, len(elst)):
+            if elst[i].startswith("NULL"):
+                break # only compare header, profile is checked separately
+            if not elst[i].startswith(('FILE', 'COM', 'DATE')):
+                self.assertEqual(elst[i], tlst[i])
+
+        prof = io.LoadSequenceProfile(hhfile, format="hhm")
+        ref_prof = io.LoadSequenceProfile("testfiles/test.hmm", format="hhm")
+
+        hmm_transitions = [seq.HMMTransition.HMM_M2M, seq.HMMTransition.HMM_M2I,
+                           seq.HMMTransition.HMM_M2D, seq.HMMTransition.HMM_I2M,
+                           seq.HMMTransition.HMM_I2I, seq.HMMTransition.HMM_D2M,
+                           seq.HMMTransition.HMM_D2D]
+        self.assertEqual(prof.sequence, ref_prof.sequence)
+        self.assertEqual(prof.neff, ref_prof.neff)
+
+        for col, ref_col in zip(prof.columns, ref_prof.columns):
+            hmm_data = col.hmm_data
+            ref_hmm_data = ref_col.hmm_data
+            self.assertAlmostEqual(hmm_data.neff, ref_hmm_data.neff, places=2)
+            self.assertAlmostEqual(hmm_data.neff_i, ref_hmm_data.neff_i,
+                                   places=2)
+            self.assertAlmostEqual(hmm_data.neff_d, ref_hmm_data.neff_d,
+                                   places=2)
+            for t in hmm_transitions:
+                self.assertAlmostEqual(hmm_data.GetProb(t),
+                                       ref_hmm_data.GetProb(t), places=2)
+            for olc in "ARNDQEKSCMWYTVILGPHF":
+                self.assertAlmostEqual(col.GetFreq(olc), ref_col.GetFreq(olc),
+                                       places=2)
         os.remove(hhfile)
 
     def testA3mToProfileWithExistingFile(self):

modules/seq/base/pymod/export_profile_handle.cc

@@ -55,7 +55,7 @@ void export_profile_handle()
     .value("HMM_D2D", HMM_D2D)
   ;
 
-  class_<HMMData>("HMMData", init<>())
+  class_<HMMData, HMMDataPtr>("HMMData", init<>())
     .add_property("neff", &HMMData::GetNeff, &HMMData::SetNeff)
     .add_property("neff_i", &HMMData::GetNeff_I, &HMMData::SetNeff_I)
     .add_property("neff_d", &HMMData::GetNeff_D, &HMMData::SetNeff_D)