diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 6ccc1e1b5940f12d7a66ee222b7c8b6b80779fa9..1c27367e2f9fbbd9ad44338ed4cc2e92060d1cf9 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/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):
diff --git a/modules/bindings/tests/testfiles/test_2.hmm b/modules/bindings/tests/testfiles/test_2.hmm
deleted file mode 100644
index 32d44862d4a908ceef0075a72513198221b2de08..0000000000000000000000000000000000000000
--- a/modules/bindings/tests/testfiles/test_2.hmm
+++ /dev/null
@@ -1,469 +0,0 @@
-HHsearch 1.5
-NAME Test
-FAM
-COM /scicore/soft/apps/HH-suite/3.2.0-foss-2018b-Boost-1.68.0-Python-3.6.6/bin/hhmake -i testfiles/testali.a3m -o testfiles/testali.hhm
-DATE Fri Mar 20 11:58:32 2020
-LENG 141 match states, 141 columns in multiple alignment
-
-FILT 112 out of 255 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20 -diff 100)
-NEFF 9.3
-SEQ
->ss_pred PSIPRED predicted secondary structure
-CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHH
-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
->ss_conf PSIPRED confidence values
-9999999999999988733915579999999986394411239877888888567889999999999987354777899999998876502999898998
-89999999997536679989999999999999999984329
->Consensus
-xltxxxxxxixxsWxxvxxxxxxxgxxxxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxvxxxlxxxixxldxxxxxlxxlxxxHxxxxgvxxxxxxx
-xxxxlxxxlxxxxgxxxxxxxxxAWxxxxxxixxxmxxxyx
->Test
-VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
-LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
->gi|1170183|sp|P42511.1|LGB_CANLI RecName: Full=Leghemoglobingi|495289|gb|AAA18503.1| leghemoglobin [Canavalia lineata]
--FSEKQESLVKSSWEAFKQNVPHHSAVFYTLILEKAPAAQNMFSFLSNGvdPNNPKLKAHAEKVFKMTVDSAVQLRAKGEVvlaDPTLGSVHV-QKGVLD
-PHFLVVKEALLKTFKEAVGDKWNDELGNAWEVAYDELAAAIKKAM-
->gi|88813510|ref|ZP_01128744.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]gi|88789223|gb|EAR20356.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]
---------LFNDSYERCIDnpNPPGFLQRFYKVFLSSSEEVAEKFKNT-------DFEKQTRVLKASLYYLMLScNGspEAMAHLRRIACLHSrKQLDIR
-PELYDLWLASLLQAAREYD-PRFDQQTETAWRQVLSHGIDFMKSRY-
->gi|336324532|ref|YP_004604499.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]gi|336108113|gb|AEI15931.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]
--VKESDLKELGSIWEQMSKYSDEFTTDMSAFVV-KNFKLPETYST-------EITDEYKAMLGKLYERVLsGRFNNDYvSFLIKFSEFNL-AYSINQEMV
-NSlisyARSWIHEKIFQNIPDDFQrKGILMMFHKIMDITGDIIISTYY
->gi|289549194|ref|YP_003474182.1| hypothetical protein Thal_1426 [Thermocrinis albus DSM 14484]gi|289182811|gb|ADC90055.1| conserved hypothetical protein [Thermocrinis albus DSM 14484]
--WTAEDEENLRSLSHLVPSWVEEFLES---------------IRK-------DEhDERCFQSIREWLIATFsGPHDERYvRKIHNMLQEHL-KAGCTLHH
-LQVllssVREFLLDKLTAQLGYSHQrDSLFRSVEKTLDLSLSIMLLSQK
->gi|341887822|gb|EGT43757.1| CBN-GLB-25 protein [Caenorhabditis brenneri]
-----RDFFTLKNWWKSVDRKRVEASTYMFSRYLNDFPENKAFYAKLkNVnAqtvdmnCSDPGFEAMAAQYLKVFDDVITAveekPGDVQSacdRLSAVGK
-MHR-AkvSGagMESSMFQNMEEPFIQMVKYILQDRFNEKAEMLYRKFFQFCLKYLLEGF-
->gi|17567933|ref|NP_509614.1| GLoBin family member (glb-17) [Caenorhabditis elegans]gi|3877381|emb|CAA86423.1| C. elegans protein F49E2.4a, partially confirmed by transcript evidence [Caenorhabditis elegans]
--ITDEEVTAIRDVWRRA--KTDNVGKKILQTLIEKRPKFAEYFGIQsESlDiralNQSKEFHLQAHRIQNFLDTAVGSLGFcpissVFDMAHRIGQIHF-
-YRGVNfgADNWLVFKKVTVDQVTtgttdsskekedtnsngtangkvdtdaSLIPiadinNVYSGencLARLGWNKLMTVIVREMKRGFL
-#
-NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
-HMM A C D E F G H I K L M N P Q R S T V W Y
- M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
- 0 * * 0 * 0 * * * *
-V 1 4902 4723 * * * 3431 3746 * 3837 * 5128 4860 1870 4923 4832 2670 5280 3268 * * 1
- 44 5066 * 2000 415 * * 6988 1000 0
-
-L 2 * * * * 3118 6092 * 3501 * 792 3848 * * * * * 6569 3621 4536 * 2
- 0 * * * * * * 8826 0 0
-
-S 3 6516 * 6204 * * * 6508 * 5652 * * 3368 6238 6481 5972 1433 1325 4717 * * 3
- 0 * * * * * * 8861 0 0
-
-P 4 3037 6170 2764 2586 * 4445 6629 5465 3966 4811 6242 * 2872 4851 4994 3922 5028 4835 * 5338 4
- 0 * * * * * * 8912 0 0
-
-A 5 2684 * 3384 2457 * 5021 6212 3905 2685 * * 5386 4978 3661 4250 3499 * * * 5368 5
- 0 * * * * * * 8946 0 0
-
-D 6 6353 * 1855 1840 * * 5446 6208 6634 6380 * 5599 * 1624 * * 5141 * * * 6
- 0 * * * * * * 8971 0 0
-
-K 7 4798 6591 * 4398 5308 * 5441 2820 2041 3610 * * * 4776 2557 * 5226 2971 5746 6354 7
- 0 * * * * * * 9237 0 0
-
-T 8 2935 * 3662 2847 5479 6921 5604 5134 2313 5429 * 5576 6602 3209 4105 4257 5027 5543 * 4469 8
- 17 * 6376 * * * * 9250 0 0
-
-N 9 2579 * 5088 4363 7129 5773 5485 3082 5829 1592 * 3594 * 6552 5667 * 3839 4146 * * 9
- 18 6337 * 0 * 0 * 9395 1049 1017
-
-V 10 4999 * * * 5673 * * 1706 * 1684 5250 * * * * * 5697 1807 * * 10
- 0 * * * * * * 9429 0 0
-
-K 11 4282 * 5528 4776 * 5343 4720 5849 2459 3699 * 4481 * 2703 1771 * 4969 5148 * * 11
- 14 * 6686 * * * * 9429 0 0
-
-A 12 3354 * 3142 3008 6297 4668 5790 * 3319 * * 3482 * 3477 3812 2383 4628 * * 6427 12
- 0 * * * * * 0 9415 0 1016
-
-A 13 3828 6340 5053 * 6520 * 5571 4774 * 4054 6421 5620 * 6689 * 1162 2255 4380 6356 * 13
- 0 * * * * * 0 9415 0 1016
-
-W 14 5645 * * 6340 3125 6297 * 5166 * 5527 6671 * * * * 6085 * 4853 528 4709 14
- 0 * * * * 0 * 9415 0 1016
-
-G 15 2813 6632 3972 2769 6609 4325 5523 6552 3445 7078 * 3444 3587 4198 4054 3274 4552 6711 * * 15
- 0 * * * * * * 9429 0 0
-
-K 16 3244 * 7059 5967 5867 5117 5470 3398 2698 3402 5964 4598 4890 4009 3205 4184 4203 3652 * 6878 16
- 29 5643 * 1000 1000 * * 9429 1188 0
-
-V 17 3752 5102 6678 * 4196 * * 2157 * 2304 3643 6616 7131 5873 5614 * 6685 1938 * * 17
- 179 4214 3998 1249 788 * * 9438 1879 0
-
-G 18 3766 7049 4191 3306 4893 5031 5890 4759 2692 4858 4741 4350 6086 4777 3462 3210 5010 5578 5230 4618 18
- 258 4118 3235 850 1168 2935 202 9332 1827 2044
-
-A 19 2910 6335 3373 3864 * 4053 5684 6256 2601 6505 6772 * 2997 3506 4283 3488 4498 6210 * * 19
- 153 4100 4568 861 1154 1073 931 9175 1746 3490
-
-H 20 5751 * 2174 4627 5269 3790 3644 5356 3245 4600 6471 2595 6360 4665 4498 5610 6922 5517 6021 4989 20
- 36 5355 * 1361 711 224 2795 9237 1215 2928
-
-A 21 3777 * 4702 5615 5098 3888 5184 4467 2604 3226 5230 5612 3495 5298 5134 3728 4896 4066 5079 4665 21
- 127 3718 6923 1356 715 * 0 9433 2199 1152
-
-G 22 3783 * 2784 2705 * 4650 5552 5227 4274 5447 7004 3897 3644 3149 4627 5558 3491 4379 * * 22
- 77 4258 * 1618 569 1040 961 9433 1771 1462
-
-E 23 3350 * 4160 1900 6504 3768 5221 5756 3864 5644 * 4326 5764 3864 3823 4167 3951 4980 * * 23
- 0 * * * * 0 * 9433 0 1152
-
-Y 24 3321 5664 6994 * 2411 * 3896 3008 * 3301 5362 3574 5612 5695 * 6063 4739 3024 6603 4118 24
- 0 * * * * * * 9438 0 0
-
-G 25 2802 6446 6086 6979 4990 939 6603 * 6452 4925 6462 * * * * 4419 3930 3627 * 6587 25
- 11 7014 * 3000 193 * * 9438 1000 0
-
-A 26 4114 6525 3406 4022 6462 6773 7035 4099 4022 3408 5885 4860 5762 3508 4219 3212 3042 3433 * * 26
- 30 5622 * 2938 202 * * 9438 1210 0
-
-E 27 3127 6446 3489 2993 6462 4760 4961 3759 3026 4286 6553 3721 * 4443 4235 4442 4065 5164 * 6398 27
- 36 6586 6152 1585 585 * * 9438 1020 0
-
-A 28 4205 5115 * * 1764 * * 1998 * 2780 3482 * * * * 6551 5856 3196 * * 28
- 0 * * * * * 0 9386 0 1125
-
-L 29 6513 * * * 1447 * 6474 * * 2521 4310 * * * * 5926 6576 5836 * 1548 29
- 0 * * * * * 0 9386 0 1125
-
-E 30 3434 * 4076 3517 5038 4990 6344 3346 3022 3127 5363 5843 * 4437 3637 3947 4034 4966 * 5350 30
- 25 5856 * 4708 56 * 0 9386 1133 1125
-
-R 31 4323 5020 5945 5130 5249 4881 5219 5126 2755 5624 6862 3533 * 4858 1655 5731 4423 5553 5225 5059 31
- 17 6448 * 3000 193 * 0 9386 1027 1125
-
-M 32 6350 6363 * * 2354 * * 3639 * 1171 3502 * * * * * 6646 3751 5575 4011 32
- 0 * * * * * 0 9385 0 1125
-
-F 33 4975 5448 * 6460 806 * 6457 4755 * 2246 4801 6653 * 5535 * * * 5304 6634 * 33
- 63 * 4558 * * * 0 9385 0 1125
-
-L 34 3330 * 4459 2124 6279 * * 6307 2936 5248 6733 3786 * 3717 4111 3393 3021 6810 * * 34
- 0 * * * * 463 1864 9210 0 1899
-
-S 35 3265 6883 3754 3319 * * 4232 4216 2663 3422 4454 4935 * 4498 3486 3684 4464 6359 * 7001 35
- 12 * 6977 * * * 0 9370 0 1125
-
-F 36 3681 5226 3589 5133 3735 * 2930 6706 4746 6808 7014 2549 * 6742 3944 3809 6926 5219 * 2624 36
- 0 * * * * 1509 624 9372 0 1290
-
-P 37 4986 * 5115 4223 5927 * 7096 6485 6673 6374 * * 436 6653 6640 4663 6452 7068 * 6396 37
- 0 * * * * * 0 9370 0 1125
-
-T 38 4121 * 2286 1986 6452 4323 5194 * 4763 4981 5558 4418 * 3947 4459 3563 5740 5505 6359 6382 38
- 0 * * * * * 0 9370 0 1125
-
-T 39 3830 5004 5876 6920 3804 * * 3285 * 2396 3829 4439 * * 6396 4375 3128 3070 6728 3479 39
- 0 * * * * * 0 9370 0 1125
-
-K 40 3900 * * 4772 * 6585 6577 4535 1889 3687 7155 6485 5927 2702 2176 6725 5604 4764 * 6907 40
- 0 * * * * * 0 9370 0 1125
-
-T 41 3167 6352 3656 2806 * 6382 * 6071 3638 4801 * 3544 3741 4601 4568 2980 3329 5659 * 5566 41
- 0 * * * * * 0 9370 0 1125
-
-Y 42 4364 * * * 3174 * 5228 3511 3000 2456 3190 * 5102 5173 5836 6883 5927 4155 * 2698 42
- 16 * 6485 * * 0 * 9370 0 1125
-
-F 43 * * * * 246 * * 5224 * 4507 6379 * * * * * * * 5256 4381 43
- 10 * 7184 * * * 0 9401 0 1043
-
-P 44 4754 * 4359 5788 * 2876 4688 * 2799 6449 6923 4035 2580 5187 4618 2987 3796 4858 * 5126 44
- 109 * 3782 * * 1241 794 9408 0 1207
-
-H 45 5622 * 4692 4241 4747 3520 4388 5590 2472 5594 5876 4333 6840 3521 3268 3820 3778 4462 6729 5086 45
- 391 4616 2347 808 1222 1276 769 9335 1555 2381
-
-F 46 3811 * 4827 6187 1414 * 6356 4681 * 2998 4009 6484 * 6302 5610 4757 3975 3846 6233 4701 46
- 1690 694 3802 168 3184 2346 316 8928 6905 4656
-
-D 47 4386 * 2057 3487 6402 2414 5438 6412 3777 5797 * 2720 * * 5362 3532 4838 * * * 47
- 154 4874 3903 668 1431 2398 304 8904 1339 4866
-
-L 48 5399 5312 5218 6425 3694 * 5533 3883 3008 2047 4152 4211 5535 5471 5267 6292 4881 2824 * 6453 48
- 649 1736 4017 728 1335 3441 139 8868 4628 4851
-
-S 49 4111 * 2584 3942 * 3932 * 6227 3198 5172 * 4699 2673 6486 * 2461 3700 6133 * 6015 49
- 2314 398 4643 2006 413 3053 185 8706 7555 5414
-
-H 50 3304 5840 5887 4083 * 6033 6349 4019 2787 3248 5537 4987 3434 3713 3001 4216 4297 6096 * * 50
- 144 3397 * 2052 398 2150 368 8593 1972 5742
-
-G 51 3203 * 4126 4322 4568 4310 5421 6652 3509 * * 3292 * 3435 4660 2294 3364 * 6538 5352 51
- 17 * 6406 * * 2982 195 8806 0 4925
-
-S 52 4926 * 2610 5957 6054 4934 5615 5282 * 6116 5459 2048 5331 6426 * 1753 4137 5358 * * 52
- 40 6184 6230 0 * 1179 840 8884 1019 4638
-
-A 53 3151 6250 4282 3262 6379 4708 5344 6550 3599 5403 * 4056 1811 5822 5681 3521 4385 * * 6695 53
- 32 * 5505 * * 809 1220 9252 0 3358
-
-Q 54 3272 6501 2954 3304 5184 3754 6710 5916 3189 5161 6483 4640 6937 3604 3367 4097 5050 4900 6449 5818 54
- 52 5219 6838 0 * 1914 445 9350 1345 2329
-
-V 55 4774 * 6129 6543 1648 * * 3404 6782 2188 3177 6501 * 7125 * 6464 5940 3247 7038 5206 55
- 17 6412 * 1585 585 1400 687 9371 1034 2104
-
-K 56 4547 6450 4826 3392 6778 4288 3868 5920 2492 4206 * 3967 * 3419 2528 4083 4767 * * 6439 56
- 0 * * * * 2419 299 9408 0 1638
-
-G 57 2498 6326 4830 3699 6126 3564 4391 6455 3628 4032 * 4135 * 4569 2909 3988 5293 5168 6982 4576 57
- 13 * 6764 * * * 0 9409 0 1489
-
-H 58 * 6139 * * 6684 * 996 6794 5468 3712 5198 * * 1884 6385 * 6552 6930 * 4729 58
- 29 * 5661 * * 1345 722 9399 0 1657
-
-G 59 1803 3789 * 5385 4751 2668 * 4963 3928 5346 5644 6561 5795 * 5702 3572 4341 3334 * * 59
- 45 6461 5670 2322 322 1331 731 9386 1026 1703
-
-K 60 3321 * 4508 3694 5494 4634 5614 4104 3050 3060 5705 4853 * 5546 3433 3896 3865 3555 * 6899 60
- 0 * * * * * 0 9373 0 1725
-
-K 61 3583 6435 * * * 6348 5334 4178 3011 4667 4294 5401 * 4071 2050 3323 3082 4474 * 6552 61
- 23 5978 * 1948 433 1276 768 9373 1141 1725
-
-V 62 * * * * 2188 * * 2332 * 2231 4254 * * * * 6458 * 1817 * 5556 62
- 0 * * * * * 0 9400 0 1360
-
-A 63 3024 5675 * * 3641 4182 * 3882 6728 2272 2975 * * 4538 5387 4379 4689 2957 6802 5695 63
- 0 * * * * 1399 688 9400 0 1360
-
-D 64 3620 5444 3823 2550 * 3549 6368 5829 3590 5078 4771 2909 * 3420 4088 4856 4307 6818 * 6561 64
- 0 * * * * 0 * 9413 0 1157
-
-A 65 2125 7471 * 6757 3747 3442 * 3967 6897 3201 4810 * * 5315 4596 3331 4021 3466 4732 5873 65
- 0 * * * * * * 9425 0 0
-
-L 66 * * * * 3355 * * 2277 * 1220 4234 * * * * * 6747 2506 * 5147 66
- 0 * * * * * * 9425 0 0
-
-T 67 4311 6893 2064 3008 * 3252 5124 5509 5767 5354 6946 3170 6577 5063 7471 3539 3962 4385 * 5970 67
- 15 6577 * 4087 87 * * 9425 1026 0
-
-N 68 3853 5810 3461 3687 4231 6957 5929 5040 3138 4178 5125 3398 6385 5637 3872 3730 3686 4723 6734 4527 68
- 0 * * * * * * 9425 0 0
-
-A 69 2441 4834 * * 3592 4566 * 2487 * 2497 4156 * * * * 4757 5515 2723 5847 5944 69
- 0 * * * * * * 9425 0 0
-
-V 70 3525 6577 * 6712 4514 * * 1706 * 3068 3883 * * * * 6582 7000 1607 * 6734 70
- 119 3653 * 1455 654 * * 9425 2384 0
-
-A 71 5064 * 2849 2879 * 3033 6671 7035 2885 5820 5752 3334 * 4104 4531 3594 4114 4538 * * 71
- 0 * * * * * * 9425 0 0
-
-H 72 3303 5864 6509 4452 5012 4870 3777 7424 3852 4273 * 2147 6168 5259 4084 2692 5257 5211 * 5197 72
- 134 3659 6712 1063 940 * * 9425 2295 0
-
-V 73 4636 5878 5223 7414 4601 * 6163 3414 5247 1190 3608 5815 4657 6413 6554 6715 5771 4219 * 4235 73
- 78 4477 7016 1162 854 0 * 9407 1719 1017
-
-D 74 4768 6566 1212 3047 7414 2771 4798 * 5855 * * 3860 5825 5147 6739 4783 5808 5949 * * 74
- 53 4796 * 1419 676 * 0 9420 1539 1000
-
-D 75 5762 * 1745 3181 5154 5798 4732 7290 3956 * * 2023 5600 4593 5057 3924 6112 * * * 75
- 437 1936 * 1771 500 0 * 9420 5055 1000
-
-M 76 3688 5873 4573 4433 4130 5321 5376 3747 5098 2138 4329 6629 2939 5831 4880 4485 5310 3870 * * 76
- 75 4577 6809 3105 178 * * 9425 1618 0
-
-P 77 3472 * 2824 2430 6643 4570 4761 5087 3852 5196 5823 5195 5987 4604 4777 3475 4449 4268 * 4565 77
- 191 3014 * 1129 882 0 * 9423 3111 1000
-
-N 78 3011 6705 5148 2566 6803 3870 5281 5499 3196 4604 * 3946 6938 4641 4631 3122 3756 4552 * 6810 78
- 298 2552 5956 1515 621 * * 9425 3845 0
-
-A 79 4608 * 7007 4521 3615 6807 5161 3323 4104 2120 3735 * 5803 5213 5554 5307 4067 3026 6590 4579 79
- 118 3669 * 1585 585 1327 734 9394 2275 1166
-
-L 80 3910 5469 6730 * 4155 * 6840 2978 4771 1214 5212 * * * 5892 5102 * 2822 6013 6369 80
- 16 6504 * 1585 585 * 0 9396 1034 1027
-
-S 81 3296 5856 4282 3929 * 7176 5375 4848 3074 4103 4710 3665 3918 3900 3580 3919 3900 4861 * 5658 81
- 10 7165 * 1585 585 0 * 9396 1000 1027
-
-A 82 3086 * 3970 3012 5082 5555 5099 * 2717 5590 6493 4744 5296 3978 3132 4027 4907 4884 * 4018 82
- 16 6493 * 1585 585 * * 9425 1034 0
-
-L 83 5506 * * 5582 4278 * * 2353 6629 1214 3367 5309 * 5909 * * 5703 3474 * 5594 83
- 39 5728 6946 964 1036 * * 9425 1202 0
-
-S 84 2425 6934 6726 4893 6474 1402 5848 5149 4967 5032 6696 4990 * * 5016 3413 5621 3671 * * 84
- 18 * 6368 * * 0 * 9417 0 1000
-
-D 85 3383 6738 4279 3223 * 4928 4406 5576 2558 5762 5491 4850 6609 2917 3220 4318 4813 5456 * 4983 85
- 0 * * * * * 0 9394 0 1104
-
-L 86 5137 * 4741 5525 5227 6588 5537 4235 3117 2440 6469 5111 6869 6932 2666 3655 3429 3280 * 6455 86
- 213 2866 * 1575 590 0 * 9394 3228 1104
-
-H 87 6572 * * 6375 * 4357 199 * * * * 5999 * 6635 * 6827 * * * 5428 87
- 0 * * * * * * 9425 0 0
-
-A 88 2536 5409 5241 5838 4449 6901 4839 4587 3189 3695 * * * 5716 2844 3759 5394 2563 6760 6933 88
- 2833 3693 354 993 1007 * * 9425 2252 0
-
-H 89 3653 4336 4648 2658 4500 * 4668 * 3460 * 4432 4473 * 4645 2592 * 2314 * * * 89
- 243 2689 * 1342 724 33 5457 6878 1372 8627
-
-K 90 3245 6569 3874 4460 4623 3462 4748 6728 2677 7032 7070 3613 4250 4325 3054 4788 4190 6026 * 6630 90
- 190 3018 * 1057 945 887 1123 9407 3174 1184
-
-L 91 4651 6412 6999 6310 3825 * 4785 4982 4859 2718 4337 5843 5254 7080 2127 4342 * 5106 * 2357 91
- 41 5147 * 1566 594 0 * 9417 1396 1000
-
-R 92 7168 6861 4335 * * 1066 5440 * 3466 * * 3614 4710 3926 3791 3915 * 6708 6650 * 92
- 81 4197 * 1980 422 * * 9425 1852 0
-
-V 93 3931 5328 * 6375 3487 * * 2053 * 2934 4200 * 5625 7016 * * * 1498 * * 93
- 37 5318 * 0 * * * 9425 1329 0
-
-D 94 4978 4977 3150 3462 * 3628 5313 6635 3195 6154 * 3582 4013 4785 4057 4744 2339 5883 * * 94
- 14 6649 * 1000 1000 * * 9425 1013 0
-
-P 95 3278 * 5392 4650 6577 3743 5203 4254 4638 4148 5353 7015 1745 4551 4383 3355 5961 4752 * * 95
- 0 * * * * * * 9425 0 0
-
-V 96 3394 * 2750 2017 5660 4495 3971 6886 3221 6884 * 6717 4786 3759 4525 5090 4454 5704 * * 96
- 0 * * * * * * 9422 0 0
-
-N 97 5724 * 3940 5910 5162 6932 2092 5646 * 3207 3795 4874 * 3471 5643 4971 6958 5068 5845 2344 97
- 0 * * * * * * 9422 0 0
-
-F 98 6475 * * * 1307 * * 3813 * 2920 4421 * 6373 * * * * 4065 3106 2769 98
- 0 * * * * * * 9422 0 0
-
-K 99 3914 * 2607 2496 * 4023 * 6309 3632 4316 7028 3079 4361 3664 4409 5812 5375 5734 5774 7048 99
- 28 5709 * 1891 453 * * 9422 1183 0
-
-L 100 3161 * 3858 3687 5860 5865 7073 3889 4782 2651 4676 3771 3910 4228 6768 4876 5044 3183 7133 6187 100
- 79 4228 * 2000 415 * * 9422 1899 0
-
-L 101 4122 * * * 1907 5923 * 3571 * 2043 3166 * * * * 6380 * 2556 5126 6586 101
- 0 * * * * * * 9422 0 0
-
-S 102 3126 5159 * 5608 4902 2054 * 4760 3130 3563 * * 6074 4562 3068 3393 6951 5626 6676 5854 102
- 14 6703 * 0 * * * 9422 1001 0
-
-H 103 4334 6647 3394 1978 * 4922 5248 6683 4142 * * 3906 4034 4216 3483 3319 4771 4652 6581 7014 103
- 0 * * * * * * 9422 0 0
-
-C 104 1778 3778 6741 6929 5236 7023 * 3278 * 4710 7016 5479 4616 4791 * 3173 5247 2625 5997 5603 104
- 0 * * * * * * 9422 0 0
-
-L 105 5621 6309 * * 2189 * * 2758 * 1279 4319 * * * * 6485 5503 3675 6703 5896 105
- 0 * * * * * * 9422 0 0
-
-L 106 5473 * 6745 7014 5661 5805 5318 2556 6570 1822 4304 * 5916 5041 4968 * 3881 2267 6706 5674 106
- 0 * * * * * * 9422 0 0
-
-V 107 3532 6453 3000 2256 4324 4080 5346 6742 4229 5357 6669 5862 5884 3840 4053 3584 5271 5792 5867 5126 107
- 0 * * * * * * 9333 0 0
-
-T 108 2621 5571 * 5083 4792 6906 5683 6379 5068 4262 4327 6664 * 6594 5498 4086 2272 2650 * 3164 108
- 0 * * * * * * 9333 0 0
-
-L 109 4799 5432 * * 2921 * * 2063 * 1621 3054 * * * * * 6379 3158 * * 109
- 44 6313 5862 1585 585 * * 9333 1087 0
-
-A 110 3297 6683 6811 2783 5105 3885 6948 5301 2965 5385 * 4866 5373 3327 2914 3685 4264 4987 * * 110
- 15 6579 * 4755 54 1003 997 9317 1013 1151
-
-A 111 3161 6557 3409 2200 6771 5939 5522 * 3422 6532 * 3963 5218 3375 4458 3182 4550 5862 * 6444 111
- 69 6749 4735 1585 585 0 * 9322 1001 1000
-
-H 112 3212 4845 * 4212 6614 5101 3751 4477 3410 3622 5667 5284 * 4282 3977 5539 4239 2674 6496 3900 112
- 106 7095 3972 0 * 0 * 9373 1000 1549
-
-L 113 5352 4370 4151 6426 3697 4849 5735 3928 6239 1367 4703 5713 * 4978 * 5419 5779 3506 6311 5022 113
- 338 4663 2563 3331 151 1148 866 9264 1542 1963
-
-P 114 4150 6214 * 4713 * 846 5704 * 3411 * 6380 * 3024 5434 6387 4673 * 6232 * * 114
- 132 4508 4521 1381 699 955 1047 9189 1503 4041
-
-A 115 3346 6541 2812 4965 * 3710 * 6588 3643 5091 * 3795 3178 4954 4391 3369 4013 3804 6361 6025 115
- 37 6250 6344 1000 1000 784 1254 9234 1046 3127
-
-E 116 3538 5000 3160 3933 7119 3548 3929 * 3088 * * 3738 5601 3780 3312 3338 5708 5001 * 6490 116
- 109 4272 5565 1382 698 1136 876 9259 1751 2035
-
-F 117 4176 6733 6850 * 2041 * 5346 3977 5248 3220 4773 6686 5750 * 5409 4262 * 4766 2478 3251 117
- 33 5457 * 4186 82 1585 585 9288 1269 1855
-
-T 118 4877 * 2285 5727 6561 5936 5528 * 4717 * * 2982 6963 5020 5257 2534 1781 * * * 118
- 108 3962 6961 778 1263 914 1092 9370 2036 1521
-
-P 119 2598 6300 2734 3577 6487 4057 4620 6920 4271 5586 6422 6112 3023 3673 4332 3496 5083 * * * 119
- 54 6552 5246 1585 585 1590 582 9389 1013 1317
-
-A 120 3202 * 2745 1904 7038 4944 * 5417 3954 5569 * 4802 6905 3208 5671 3297 4594 6546 * * 120
- 27 6614 6959 2000 415 * 0 9358 1002 1644
-
-V 121 2588 5448 5835 5246 6759 7629 5903 3111 * 2828 5053 6329 * 3963 6445 4939 2516 2789 * 6770 121
- 0 * * * * 2611 258 9353 0 1798
-
-H 122 3479 * 4791 2168 6135 5731 6829 4176 2729 3657 5544 6606 6646 3768 3705 * 4199 3678 * * 122
- 0 * * * * 0 * 9358 0 1644
-
-A 123 2950 * 3385 2361 * 3932 5625 6791 3549 4564 4793 4781 * 4136 3611 3995 3994 5567 * * 123
- 12 6919 * 1585 585 * * 9333 1000 0
-
-S 124 723 * * 5756 * 4665 * 4527 * 5009 5975 * * * 6677 2836 4178 4975 6759 * 124
- 11 7016 * 3000 193 * * 9333 1000 0
-
-L 125 5652 * * * 3969 * * * * 4262 5034 * * * * * * 5441 357 5057 125
- 0 * * * * * * 9333 0 0
-
-D 126 3795 * 3376 3576 * 4559 4916 4510 2934 4630 4979 3787 * 5121 2700 3799 3591 6011 * * 126
- 0 * * * * * * 9333 0 0
-
-K 127 4016 5519 3926 3827 6541 4812 5734 5779 1446 4315 * 5253 * 4143 4090 4792 4130 4484 * * 127
- 0 * * * * * * 9333 0 0
-
-F 128 2344 4789 * * 2941 5045 * 3311 * 2003 4114 * * * * 6723 3978 3095 * 6878 128
- 0 * * * * * * 9333 0 0
-
-L 129 6609 * * * 2250 5799 * 3505 * 1874 3431 5201 * * * 6680 5175 4267 4290 2832 129
- 14 6744 * 0 * * * 9333 1000 0
-
-A 130 3258 * 2255 4171 * 3221 6959 * 3195 6778 6451 4511 6603 3967 3964 3035 3992 6604 6943 * 130
- 13 * 6817 * * * * 9333 0 0
-
-S 131 4190 5659 5971 4777 2794 5404 4955 3447 6769 3536 7272 4262 6646 6623 4517 4415 4363 2877 * 2923 131
- 10 7123 * 2000 415 * 0 9285 1000 1008
-
-V 132 5083 5828 * * 3010 5659 * 1725 * 2647 4814 6283 * * * 5279 4723 2137 7068 * 132
- 0 * * 1585 585 0 * 9293 1008 1008
-
-S 133 2672 4251 6697 5449 3979 3897 * 2654 * 3468 5786 5251 * 5726 4839 4137 4138 2908 * 4907 133
- 15 * 6571 * * * * 9247 0 0
-
-T 134 3243 6371 2143 3708 5671 4046 5018 5781 3728 5029 * 3580 5706 5260 4948 3907 3732 5983 * 5323 134
- 17 6406 * 0 * 0 * 9232 1014 1001
-
-V 135 3056 6531 5849 4454 5747 4093 4646 3281 5097 3438 4550 * 6534 4346 3835 4945 3719 2842 * 4513 135
- 0 * * * * * * 9223 0 0
-
-L 136 6586 * * * 4363 * 6711 1952 * 1675 1668 * * 6652 * * * 4824 * * 136
- 15 6620 * 2000 415 * * 9187 1000 0
-
-T 137 3670 5671 5754 4564 4270 3863 * 3988 2197 3366 6501 7328 * 5195 3530 3698 4215 3638 * * 137
- 0 * * * * * * 9145 0 0
-
-S 138 3032 * 4301 2873 6167 4852 4000 6243 4509 4502 * 5055 * 3868 4323 2107 5376 4017 * 6410 138
- 20 6167 * 2000 415 * * 9050 1002 0
-
-K 139 2586 * * 3753 5978 1483 5001 6010 3707 5050 * * * 4364 5940 3818 4317 * * 4435 139
- 0 * * * * * * 8790 0 0
-
-Y 140 4354 5611 * * 2745 5871 * 4830 * 4204 3239 * * 4680 * 5736 * 6341 5561 1066 140
- 0 * * * * * * 8524 0 0
-
-R 141 3833 * 4287 3877 * * 4777 * 1861 3758 * * * 4873 2285 3881 * 4747 * 3635 141
- 0 * * 0 * * * 7263 0 0
-
-//
diff --git a/modules/seq/base/pymod/export_profile_handle.cc b/modules/seq/base/pymod/export_profile_handle.cc
index 949db395363f6472ef908c49e0b774bbc3e8aea9..b6208b6d74fdb0892784d0984b1a72714b58922e 100644
--- a/modules/seq/base/pymod/export_profile_handle.cc
+++ b/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)