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comparison commons/pyRepetUnit/profilesDB/tests/TestProfiles.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import os
2 import unittest
3 from commons.pyRepetUnit.profilesDB.Profiles import Profiles
4 from commons.core.utils.FileUtils import FileUtils
5
6
7 class TestProfiles(unittest.TestCase):
8
9 def createInputDBFile(self):
10 f = open(self._inputDBFile, "w")
11 f.write("HMMER2.0 [2.3.2]\n")
12 f.write("NAME fn3\n")
13 f.write("ACC PF00041\n")
14 f.write("DESC Fibronectin type III domain\n")
15 f.write("LENG 84\n")
16 f.write("ALPH Amino\n")
17 f.write("RF no\n")
18 f.write("CS yes\n")
19 f.write("MAP yes\n")
20 f.write("COM hmmbuild -A myhmms fn3.sto\n")
21 f.write("COM hmmcalibrate myhmms\n")
22 f.write("NSEQ 108\n")
23 f.write("DATE Thu Jan 8 17:50:26 2009\n")
24 f.write("CKSUM 6130\n")
25 f.write("GA 7.8 2.0;\n")
26 f.write("TC 7.9 2.1;\n")
27 f.write("NC 7.0 1.1;\n")
28 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
29 f.write("NULT -4 -8455\n")
30 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
31 f.write("EVD -45.973442 0.237545\n")
32 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
33 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
34 f.write("COM hmmcalibrate myhmms\n")
35 f.write(" -13 * -6756\n")
36 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")
37 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
38 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
39 f.write("//\n")
40 f.write("HMMER2.0 [2.3.2]\n")
41 f.write("NAME truc\n")
42 f.write("ACC PF00042.012\n")
43 f.write("LENG 123\n")
44 f.write("ALPH Amino\n")
45 f.write("RF no\n")
46 f.write("CS yes\n")
47 f.write("MAP yes\n")
48 f.write("COM hmmbuild -A myhmms fn3.sto\n")
49 f.write("COM hmmcalibrate myhmms\n")
50 f.write("NSEQ 108\n")
51 f.write("DATE Thu Jan 8 17:50:26 2009\n")
52 f.write("CKSUM 6130\n")
53 f.write("GA 7.8 -1.0;\n")
54 f.write("TC 7.9 0.1;\n")
55 f.write("NC 7.8 0.1;\n")
56 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
57 f.write("NULT -4 -8455\n")
58 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
59 f.write("EVD -45.973442 0.237545\n")
60 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
61 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
62 f.write("COM hmmcalibrate myhmms\n")
63 f.write(" -13 * -6756\n")
64 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")
65 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
66 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
67 f.write("//\n")
68 f.close()
69
70
71 def setUp(self):
72 self.profiles = Profiles()
73 self._inputDBFile = "dummy.hmm"
74
75
76 def testRead(self):
77 # atomic profiles file
78 self.createInputDBFile()
79 file = open( self._inputDBFile )
80 profile = self.profiles
81 profile.read(file)
82 self.assertEqual("fn3",profile.name)
83 self.assertEqual("Fibronectin type III domain", profile.desc)
84 self.assertEqual(84, profile.length)
85 self.assertEqual("PF00041", profile.accNumber)
86 self.assertEqual(2.0, profile.GA_cut_off)
87 profile.read(file)
88 self.assertEqual("truc",profile.name)
89 self.assertEqual("", profile.desc)
90 self.assertEqual(123, profile.length)
91 self.assertEqual("PF00042.012", profile.accNumber)
92 self.assertEqual(-1.0, profile.GA_cut_off)
93 os.system("rm " + self._inputDBFile)
94 # empty file
95 f = open(self._inputDBFile, "w")
96 f.close()
97 file = open( self._inputDBFile )
98 profile = self.profiles
99 profile.read(file)
100 self.assertEqual(None, profile.name)
101 self.assertEqual(None, profile.desc)
102 self.assertEqual(None, profile.length)
103 self.assertEqual(None, profile.accNumber)
104 self.assertEqual(None, profile.GA_cut_off)
105 os.system("rm " + self._inputDBFile)
106
107
108 def testReadAndRetrieve(self):
109 # atomic profiles file
110 self.createInputDBFile()
111 file = open( self._inputDBFile )
112 profile = self.profiles
113 myProfile = profile.readAndRetrieve(file)
114 self.assertEqual("fn3",profile.name)
115 self.assertEqual("Fibronectin type III domain", profile.desc)
116 self.assertEqual(84, profile.length)
117 self.assertEqual("PF00041", profile.accNumber)
118 self.assertEqual(2.0, profile.GA_cut_off)
119 myProfile2 = profile.readAndRetrieve(file)
120 self.assertEqual("truc",profile.name)
121 self.assertEqual("", profile.desc)
122 self.assertEqual(123, profile.length)
123 self.assertEqual("PF00042.012", profile.accNumber)
124 self.assertEqual(-1.0, profile.GA_cut_off)
125 #I check if retrieve work like I want
126 f = open("retrieveResult", "w")
127 for item in myProfile:
128 f.write(item)
129 for item in myProfile2:
130 f.write(item)
131 f.close()
132 self.assertTrue(FileUtils.are2FilesIdentical("retrieveResult", self._inputDBFile))
133 os.system("rm " + self._inputDBFile)
134 os.system("rm retrieveResult")
135 # empty file
136 f = open(self._inputDBFile, "w")
137 f.close()
138 file = open( self._inputDBFile )
139 profile = self.profiles
140 myProfile3 = profile.readAndRetrieve(file)
141 self.assertEqual(None, profile.name)
142 self.assertEqual(None, profile.desc)
143 self.assertEqual(None, profile.length)
144 self.assertEqual(None, profile.accNumber)
145 self.assertEqual(None, profile.GA_cut_off)
146 self.assertEqual(None, myProfile3)
147 os.system("rm " + self._inputDBFile)
148
149
150 if __name__ == "__main__":
151 unittest.main()