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Commit b69553b6 authored by Studer Gabriel's avatar Studer Gabriel
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adapt unit tests to HHblits 3 

- Use new HHblits database in testfiles
- adapt to new file structure (location of cs219.lib)
- generate new files for comparison
  => content of HHblits database changed and some ordering of lines
     is different in HHblits 3 anyways. However, that might be highly
     version specific
parent 4f32afa7
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modules/bindings/tests/test_hhblits.py
+ 9
− 11
View file @ b69553b6
...@@ -132,8 +132,8 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -132,8 +132,8 @@ class TestHHblitsBindings(unittest.TestCase):
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR') 'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot) self.hh = hhblits.HHblits(query_seq, self.hhroot)
a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/hhblitsdb') a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/unittestdb')
self.assertTrue(filecmp.cmp(a3m, "testfiles/testali.a3m")) self.assertTrue(filecmp.cmp(a3m, "testfiles/testali_two.a3m"))
def testA3mToProfileFileName(self): def testA3mToProfileFileName(self):
# test A3mToProfile to work with a given hhmake_file name # test A3mToProfile to work with a given hhmake_file name
...@@ -215,7 +215,7 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -215,7 +215,7 @@ class TestHHblitsBindings(unittest.TestCase):
os.remove(self.tmpfile) os.remove(self.tmpfile)
csfile = self.hh.A3MToCS("testfiles/testali.a3m", csfile = self.hh.A3MToCS("testfiles/testali.a3m",
cs_file=self.tmpfile, options={'-alphabet' : cs_file=self.tmpfile, options={'-alphabet' :
os.path.join(self.hh.hhlib_dir, os.path.join(self.hhroot,
'data', 'data',
'cs219.lib')}) 'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219')) self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
...@@ -230,7 +230,7 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -230,7 +230,7 @@ class TestHHblitsBindings(unittest.TestCase):
self.hh = hhblits.HHblits(query_seq, self.hhroot) self.hh = hhblits.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m", csfile = self.hh.A3MToCS("testfiles/testali.a3m",
options={'-alphabet' : options={'-alphabet' :
os.path.join(self.hh.hhlib_dir, os.path.join(self.hhroot,
'data', 'data',
'cs219.lib')}) 'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219')) self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
...@@ -247,7 +247,7 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -247,7 +247,7 @@ class TestHHblitsBindings(unittest.TestCase):
csfile = self.hh.A3MToCS("testfiles/testali.a3m", csfile = self.hh.A3MToCS("testfiles/testali.a3m",
cs_file='testfiles/test.seq219', cs_file='testfiles/test.seq219',
options={'-alphabet' : options={'-alphabet' :
os.path.join(self.hh.hhlib_dir, os.path.join(self.hhroot,
'data', 'data',
'cs219.lib')}) 'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219')) self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
...@@ -261,11 +261,11 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -261,11 +261,11 @@ class TestHHblitsBindings(unittest.TestCase):
'TSKYR') 'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot) self.hh = hhblits.HHblits(query_seq, self.hhroot)
search_file = self.hh.Search("testfiles/testali.a3m", search_file = self.hh.Search("testfiles/testali.a3m",
'testfiles/hhblitsdb/hhblitsdb') 'testfiles/hhblitsdb/unittestdb')
with open(search_file) as tfh: with open(search_file) as tfh:
tlst = tfh.readlines() tlst = tfh.readlines()
with open("testfiles/test.hhr") as efh: with open("testfiles/test_two.hhr") as efh:
elst = efh.readlines() elst = efh.readlines()
self.assertEqual(len(elst), len(tlst)) self.assertEqual(len(elst), len(tlst))
...@@ -274,16 +274,14 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -274,16 +274,14 @@ class TestHHblitsBindings(unittest.TestCase):
self.assertEqual(elst[i], tlst[i]) self.assertEqual(elst[i], tlst[i])
def testSearchNotWorking(self): def testSearchNotWorking(self):
# successful search
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR') 'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot) self.hh = hhblits.HHblits(query_seq, self.hhroot)
search_file = self.hh.Search("doesnotexist.a3m", with self.assertRaises(RuntimeError) as rte:
'testfiles/hhblitsdb/hhblitsdb') self.hh.Search("doesnotexist.a3m", 'testfiles/hhblitsdb/unittestdb')
self.assertEqual(search_file, None)
def testParseHHMWorking(self): def testParseHHMWorking(self):
# get info from an HHM file # get info from an HHM file
......
modules/bindings/tests/testfiles/test_two.hhr 0 → 100644
+ 80
− 0
View file @ b69553b6
Query Test
Match_columns 141
No_of_seqs 253 out of 255
Neff 9.40349
Searched_HMMs 5
Date Thu Apr 16 22:48:40 2020
Command /scicore/soft/apps/HH-suite/3.2.0-foss-2018b-Boost-1.68.0-Python-3.6.6/bin/hhblits -cpu 1 -n 1 -e 0.001 -Z 10000 -B 10000 -i /scicore/home/schwede/studga00/prog/ost_dev/modules/bindings/tests/testfiles/testali.a3m -o /scratch/tmpc2d8_x_x/testali_cpu1_n1.hhr -d /scicore/home/schwede/studga00/prog/ost_dev/modules/bindings/tests/testfiles/hhblitsdb/unittestdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 Test 100.0 4.3E-39 9E-41 199.3 18.3 141 1-141 1-141 (141)
2 Test 1.6 3.2 0.068 12.3 1.6 10 9-18 120-129 (141)
3 fff405e08062fd0869ae7b125b27b3 0.2 24 0.51 11.5 6.8 18 29-46 320-337 (848)
4 fffff7f3b4369f17341d1230f9b841 0.0 28 0.6 8.1 -1.9 13 115-127 133-145 (195)
No 1
>Test
Probab=100.00 E-value=4.3e-39 Score=199.35 Aligned_cols=141 Identities=100% Similarity=1.413 Sum_probs=132.9 Template_Neff=9.300
Q ss_pred CCCHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhCccccccCCCCCCCCCChhHHHHHHHHHHHHHHHHhccCCHHHHH
Q Test 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL 80 (141)
Q Consensus 1 ~lt~~~~~~i~~sW~~v~~~~~~~g~~~f~~lf~~~P~~~~~F~~~~~~~~~~~~~~h~~~v~~~l~~~i~~ld~~~~~l 80 (141)
+||++|+++|++||+.+.++.+++|..||.+||+.+|+++.+|+.++.+.+||.++.|+.+|+++|+.+|+++|++...+
T Consensus 1 ~lt~~~~~~i~~sW~~v~~~~~~~g~~~~~~lf~~~P~~~~~F~~~~~~~~~~~~~~h~~~v~~~l~~~i~~ld~~~~~l 80 (141)
T Test 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL 80 (141)
T ss_pred CCCHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhCccccccCCCCCCCCCChhHHHHHHHHHHHHHHHHhccCCHHHHH
Confidence 68999999999999999888899999999999999999999999873335778999999999999999999999998899
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhcC
Q Test 81 SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
Q Consensus 81 ~~l~~~H~~~~gv~~~~f~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~m~~~~~ 141 (141)
..+|+.|.+++||+|+||+.++++|+++|++.+|++||+++++||++++++|++.|.++|+
T Consensus 81 ~~l~~~H~~~~gv~~~~~~~~~~~l~~~l~~~~g~~~~~~~~~AW~~~~~~i~~~m~~~y~ 141 (141)
T Test 81 SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
T ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhcC
Confidence 9999999735999999999999999999999999999999999999999999999999985
No 2
>Test
Probab=1.57 E-value=3.2 Score=12.26 Aligned_cols=10 Identities=30% Similarity=0.185 Sum_probs=6.4 Template_Neff=9.300
Q ss_pred HHHHHHHHHh
Q Test 9 NVKAAWGKVG 18 (141)
Q Consensus 9 ~i~~sW~~v~ 18 (141)
.+..+|..+.
T Consensus 120 ~~~~AW~~~~ 129 (141)
T Test 120 AVHASLDKFL 129 (141)
T ss_pred HHHHHHHHHH
Confidence 3566777764
No 3
>fff405e08062fd0869ae7b125b27b353
Probab=0.20 E-value=24 Score=11.45 Aligned_cols=18 Identities=6% Similarity=0.048 Sum_probs=12.1 Template_Neff=9.500
Q ss_pred HHHHHhhCccccccCCCC
Q Test 29 LERMFLSFPTTKTYFPHF 46 (141)
Q Consensus 29 f~~lf~~~P~~~~~F~~~ 46 (141)
|.++++.+|.+...|..+
T Consensus 320 ~~~~~~~~~~l~~rf~~i 337 (848)
T fff405e08062fd 320 YRKHIEKDAALERRFQQV 337 (848)
T ss_pred HHHHHhcChhHhhcCeee
Confidence 456666777777777654
No 4
>fffff7f3b4369f17341d1230f9b841ec
Probab=0.04 E-value=28 Score=8.14 Aligned_cols=13 Identities=23% Similarity=0.414 Sum_probs=7.6 Template_Neff=7.400
Q ss_pred cCCCHHHHHHHHH
Q Test 115 AEFTPAVHASLDK 127 (141)
Q Consensus 115 ~~~~~~~~~AW~~ 127 (141)
.+|.+.....|..
T Consensus 133 ~~F~p~~~~~~~~ 145 (195)
T fffff7f3b4369f 133 TDFDSQTNVSQSK 145 (195)
T ss_pred ecCCCCCceeeec
Confidence 4566665566643
modules/bindings/tests/testfiles/testali_two.a3m 0 → 100644
+ 228
− 0
View file @ b69553b6
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