|
18
|
1 import os
|
|
|
2 import unittest
|
|
|
3 from commons.pyRepetUnit.profilesDB.Profiles import Profiles
|
|
|
4 from commons.pyRepetUnit.profilesDB.ProfilesDatabank import ProfilesDatabank
|
|
|
5 import commons.pyRepetUnit.profilesDB.ProfilesDB2Map
|
|
|
6 from commons.core.utils.FileUtils import FileUtils
|
|
|
7
|
|
|
8
|
|
|
9 class TestProfilesDB2Map(unittest.TestCase):
|
|
|
10
|
|
|
11 def setUp(self):
|
|
|
12 self.profilesDB2Map = commons.pyRepetUnit.profilesDB.ProfilesDB2Map.ProfilesDB2Map()
|
|
|
13
|
|
|
14
|
|
|
15 def testWriteProfilesDB(self):
|
|
|
16 # atomic hmmerpfam file
|
|
|
17 profilesDB = ProfilesDatabank()
|
|
|
18 profiles1 = Profiles()
|
|
|
19 profiles1.name = "fn3"
|
|
|
20 profiles1.desc = "Fibronectin type III domain"
|
|
|
21 profiles1.length = 84
|
|
|
22 profilesDB.append( profiles1 )
|
|
|
23 profiles2 = Profiles()
|
|
|
24 profiles2.name = "truc"
|
|
|
25 profiles2.desc = ""
|
|
|
26 profiles2.length = 123
|
|
|
27 profilesDB.append( profiles2 )
|
|
|
28 file = open( "expectedFile", "w" )
|
|
|
29 file.write( "fn3\tFibronectin type III domain\t1\t84\n" )
|
|
|
30 file.write( "truc\t\t1\t123\n" )
|
|
|
31 file.close()
|
|
|
32 self.profilesDB2Map.setOutputFile("testOutput.map")
|
|
|
33 self.profilesDB2Map._writeMapFile(profilesDB)
|
|
|
34 self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map"))
|
|
|
35 os.remove("expectedFile")
|
|
|
36 os.remove("testOutput.map")
|
|
|
37 #empty profileDB object
|
|
|
38 profilesDB = ProfilesDatabank()
|
|
|
39 self.profilesDB2Map._writeMapFile(profilesDB)
|
|
|
40 self.assertFalse(FileUtils.isRessourceExists("testOutput.map"))
|
|
|
41
|
|
|
42 def testReadProfilesDB(self):
|
|
|
43 # atomic hmmerpfam file
|
|
|
44 f = open("dummy.hmm", "w")
|
|
|
45 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
46 f.write("NAME fn3\n")
|
|
|
47 f.write("ACC PF00041\n")
|
|
|
48 f.write("DESC Fibronectin type III domain\n")
|
|
|
49 f.write("LENG 84\n")
|
|
|
50 f.write("ALPH Amino\n")
|
|
|
51 f.write("RF no\n")
|
|
|
52 f.write("CS yes\n")
|
|
|
53 f.write("MAP yes\n")
|
|
|
54 f.write("COM hmmbuild -A myhmms fn3.sto\n")
|
|
|
55 f.write("COM hmmcalibrate myhmms\n")
|
|
|
56 f.write("NSEQ 108\n")
|
|
|
57 f.write("DATE Thu Jan 8 17:50:26 2009\n")
|
|
|
58 f.write("CKSUM 6130\n")
|
|
|
59 f.write("GA 7.8 -1.0\n")
|
|
|
60 f.write("TC 7.9 0.1\n")
|
|
|
61 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
|
|
|
62 f.write("NULT -4 -8455\n")
|
|
|
63 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
|
|
|
64 f.write("EVD -45.973442 0.237545\n")
|
|
|
65 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
|
|
|
66 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
67 f.write("COM hmmcalibrate myhmms\n")
|
|
|
68 f.write(" -13 * -6756\n")
|
|
|
69 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")
|
|
|
70 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
|
|
|
71 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
|
|
|
72 f.write("//\n")
|
|
|
73 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
74 f.write("NAME truc\n")
|
|
|
75 f.write("ACC PF00041\n")
|
|
|
76 f.write("LENG 123\n")
|
|
|
77 f.write("ALPH Amino\n")
|
|
|
78 f.write("RF no\n")
|
|
|
79 f.write("CS yes\n")
|
|
|
80 f.write("MAP yes\n")
|
|
|
81 f.write("COM hmmbuild -A myhmms fn3.sto\n")
|
|
|
82 f.write("COM hmmcalibrate myhmms\n")
|
|
|
83 f.write("NSEQ 108\n")
|
|
|
84 f.write("DATE Thu Jan 8 17:50:26 2009\n")
|
|
|
85 f.write("CKSUM 6130\n")
|
|
|
86 f.write("GA 7.8 -1.0\n")
|
|
|
87 f.write("TC 7.9 0.1\n")
|
|
|
88 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
|
|
|
89 f.write("NULT -4 -8455\n")
|
|
|
90 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
|
|
|
91 f.write("EVD -45.973442 0.237545\n")
|
|
|
92 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
|
|
|
93 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
94 f.write("COM hmmcalibrate myhmms\n")
|
|
|
95 f.write(" -13 * -6756\n")
|
|
|
96 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")
|
|
|
97 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
|
|
|
98 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
|
|
|
99 f.write("//\n")
|
|
|
100 f.close()
|
|
|
101 self.profilesDB2Map.setInputFile("dummy.hmm")
|
|
|
102 pfamDB = self.profilesDB2Map._readProfilesDB()
|
|
|
103 expectedProfiles1 = Profiles()
|
|
|
104 expectedProfiles1.name = "fn3"
|
|
|
105 expectedProfiles1.desc = "Fibronectin type III domain"
|
|
|
106 expectedProfiles1.length = 84
|
|
|
107 expectedProfiles2 = Profiles()
|
|
|
108 expectedProfiles2.name = "truc"
|
|
|
109 expectedProfiles2.desc = ""
|
|
|
110 expectedProfiles2.length = 123
|
|
|
111 self.assertEqual(expectedProfiles1.name, pfamDB.get(0).name)
|
|
|
112 self.assertEqual(expectedProfiles1.desc, pfamDB.get(0).desc)
|
|
|
113 self.assertEqual(expectedProfiles1.length, pfamDB.get(0).length)
|
|
|
114 self.assertEqual(expectedProfiles2.name, pfamDB.get(1).name)
|
|
|
115 self.assertEqual(expectedProfiles2.desc, pfamDB.get(1).desc)
|
|
|
116 self.assertEqual(expectedProfiles2.length, pfamDB.get(1).length)
|
|
|
117 os.remove("dummy.hmm")
|
|
|
118 #empty pfamDB file
|
|
|
119 file = open( "pfamDBEmpty", "w" )
|
|
|
120 file.close()
|
|
|
121 self.profilesDB2Map.setInputFile("pfamDBEmpty")
|
|
|
122 pfamDB2 = self.profilesDB2Map._readProfilesDB()
|
|
|
123 self.assertEquals(None, pfamDB2)
|
|
|
124 os.system("rm pfamDBEmpty")
|
|
|
125
|
|
|
126 def testRun(self):
|
|
|
127 f = open("dummy.hmm", "w")
|
|
|
128 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
129 f.write("NAME fn3\n")
|
|
|
130 f.write("ACC PF00041\n")
|
|
|
131 f.write("DESC Fibronectin type III domain\n")
|
|
|
132 f.write("LENG 84\n")
|
|
|
133 f.write("ALPH Amino\n")
|
|
|
134 f.write("RF no\n")
|
|
|
135 f.write("CS yes\n")
|
|
|
136 f.write("MAP yes\n")
|
|
|
137 f.write("COM hmmbuild -A myhmms fn3.sto\n")
|
|
|
138 f.write("COM hmmcalibrate myhmms\n")
|
|
|
139 f.write("NSEQ 108\n")
|
|
|
140 f.write("DATE Thu Jan 8 17:50:26 2009\n")
|
|
|
141 f.write("CKSUM 6130\n")
|
|
|
142 f.write("GA 7.8 -1.0\n")
|
|
|
143 f.write("TC 7.9 0.1\n")
|
|
|
144 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
|
|
|
145 f.write("NULT -4 -8455\n")
|
|
|
146 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
|
|
|
147 f.write("EVD -45.973442 0.237545\n")
|
|
|
148 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
|
|
|
149 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
150 f.write("COM hmmcalibrate myhmms\n")
|
|
|
151 f.write(" -13 * -6756\n")
|
|
|
152 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")
|
|
|
153 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
|
|
|
154 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
|
|
|
155 f.write("//\n")
|
|
|
156 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
157 f.write("NAME truc\n")
|
|
|
158 f.write("ACC PF00041\n")
|
|
|
159 f.write("LENG 123\n")
|
|
|
160 f.write("ALPH Amino\n")
|
|
|
161 f.write("RF no\n")
|
|
|
162 f.write("CS yes\n")
|
|
|
163 f.write("MAP yes\n")
|
|
|
164 f.write("COM hmmbuild -A myhmms fn3.sto\n")
|
|
|
165 f.write("COM hmmcalibrate myhmms\n")
|
|
|
166 f.write("NSEQ 108\n")
|
|
|
167 f.write("DATE Thu Jan 8 17:50:26 2009\n")
|
|
|
168 f.write("CKSUM 6130\n")
|
|
|
169 f.write("GA 7.8 -1.0\n")
|
|
|
170 f.write("TC 7.9 0.1\n")
|
|
|
171 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
|
|
|
172 f.write("NULT -4 -8455\n")
|
|
|
173 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
|
|
|
174 f.write("EVD -45.973442 0.237545\n")
|
|
|
175 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
|
|
|
176 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
177 f.write("COM hmmcalibrate myhmms\n")
|
|
|
178 f.write(" -13 * -6756\n")
|
|
|
179 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")
|
|
|
180 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
|
|
|
181 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
|
|
|
182 f.write("//\n")
|
|
|
183 f.close()
|
|
|
184 self.profilesDB2Map.setInputFile("dummy.hmm")
|
|
|
185 self.profilesDB2Map.setOutputFile("testOutput.map")
|
|
|
186 self.profilesDB2Map.run()
|
|
|
187 file = open( "expectedFile", "w" )
|
|
|
188 file.write( "fn3\tFibronectin type III domain\t1\t84\n" )
|
|
|
189 file.write( "truc\t\t1\t123\n" )
|
|
|
190 file.close()
|
|
|
191 self.assertTrue(FileUtils.are2FilesIdentical("expectedFile", "testOutput.map"))
|
|
|
192 os.remove("expectedFile")
|
|
|
193 os.remove("testOutput.map")
|
|
|
194 os.remove("dummy.hmm")
|
|
|
195
|
|
|
196
|
|
|
197 if __name__ == "__main__":
|
|
|
198 unittest.main()
|
|
|
199 |
