Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/profilesDB/tests/TestProfilesDatabankUtils.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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1 import unittest | |
2 import os | |
3 from commons.pyRepetUnit.profilesDB.Profiles import Profiles | |
4 from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils | |
5 | |
6 | |
7 class TestProfilesDatabankUtils( unittest.TestCase ): | |
8 | |
9 def setUp( self ): | |
10 self.profilesDBUtils = ProfilesDatabankUtils() | |
11 | |
12 | |
13 def test_read_emptyFile( self ): | |
14 file = open( "pfamDBEmpty", "w" ) | |
15 file.close() | |
16 pfamDB2 = self.profilesDBUtils.read( "pfamDBEmpty" ) | |
17 self.assertEquals( None, pfamDB2 ) | |
18 os.remove( "pfamDBEmpty" ) | |
19 | |
20 | |
21 def test_read( self ): | |
22 f = open("dummy.hmm", "w") | |
23 f.write("HMMER2.0 [2.3.2]\n") | |
24 f.write("NAME fn3\n") | |
25 f.write("ACC PF00041\n") | |
26 f.write("DESC Fibronectin type III domain\n") | |
27 f.write("LENG 84\n") | |
28 f.write("ALPH Amino\n") | |
29 f.write("RF no\n") | |
30 f.write("CS yes\n") | |
31 f.write("MAP yes\n") | |
32 f.write("COM hmmbuild -A myhmms fn3.sto\n") | |
33 f.write("COM hmmcalibrate myhmms\n") | |
34 f.write("NSEQ 108\n") | |
35 f.write("DATE Thu Jan 8 17:50:26 2009\n") | |
36 f.write("CKSUM 6130\n") | |
37 f.write("GA 7.8 -1.0\n") | |
38 f.write("TC 7.9 0.1\n") | |
39 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") | |
40 f.write("NULT -4 -8455\n") | |
41 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") | |
42 f.write("EVD -45.973442 0.237545\n") | |
43 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") | |
44 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") | |
45 f.write("COM hmmcalibrate myhmms\n") | |
46 f.write(" -13 * -6756\n") | |
47 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") | |
48 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") | |
49 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") | |
50 f.write("//\n") | |
51 f.write("HMMER2.0 [2.3.2]\n") | |
52 f.write("NAME truc\n") | |
53 f.write("ACC PF00041\n") | |
54 f.write("LENG 123\n") | |
55 f.write("ALPH Amino\n") | |
56 f.write("RF no\n") | |
57 f.write("CS yes\n") | |
58 f.write("MAP yes\n") | |
59 f.write("COM hmmbuild -A myhmms fn3.sto\n") | |
60 f.write("COM hmmcalibrate myhmms\n") | |
61 f.write("NSEQ 108\n") | |
62 f.write("DATE Thu Jan 8 17:50:26 2009\n") | |
63 f.write("CKSUM 6130\n") | |
64 f.write("GA 7.8 -1.0\n") | |
65 f.write("TC 7.9 0.1\n") | |
66 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") | |
67 f.write("NULT -4 -8455\n") | |
68 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") | |
69 f.write("EVD -45.973442 0.237545\n") | |
70 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") | |
71 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") | |
72 f.write("COM hmmcalibrate myhmms\n") | |
73 f.write(" -13 * -6756\n") | |
74 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n") | |
75 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") | |
76 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") | |
77 f.write("//\n") | |
78 f.close() | |
79 pfamDB = self.profilesDBUtils.read("dummy.hmm") | |
80 expectedProfiles1 = Profiles() | |
81 expectedProfiles1.name = "fn3" | |
82 expectedProfiles1.desc = "Fibronectin type III domain" | |
83 expectedProfiles1.length = 84 | |
84 expectedProfiles2 = Profiles() | |
85 expectedProfiles2.name = "truc" | |
86 expectedProfiles2.desc = "" | |
87 expectedProfiles2.length = 123 | |
88 | |
89 self.assertEqual( expectedProfiles1.name, pfamDB.get(0).name ) | |
90 self.assertEqual( expectedProfiles1.desc, pfamDB.get(0).desc ) | |
91 self.assertEqual( expectedProfiles1.length, pfamDB.get(0).length ) | |
92 self.assertEqual( expectedProfiles2.name, pfamDB.get(1).name ) | |
93 self.assertEqual( expectedProfiles2.desc, pfamDB.get(1).desc ) | |
94 self.assertEqual( expectedProfiles2.length, pfamDB.get(1).length ) | |
95 | |
96 os.remove("dummy.hmm") | |
97 | |
98 | |
99 if __name__ == "__main__": | |
100 unittest.main() | |
101 |