Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/profilesDB/tests/Test_ProfilesDB4Repet.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 unittest
2 import os
3 from commons.pyRepetUnit.profilesDB.ProfilesDB4Repet import ProfilesDB4Repet
4 from commons.core.utils.FileUtils import FileUtils
5
6
7 class Test_ProfilesDB4Repet(unittest.TestCase):
8
9 def setUp(self):
10 self._inputDBFile = "./datas/dummy.hmm"
11 self._expectedDBFile = "./datas/expected.hmm"
12 self._outputDBFile = "./datas/output.hmm"
13 self._profilesDB4Repet = ProfilesDB4Repet()
14
15 def tearDown(self):
16 os.remove(self._expectedDBFile)
17 os.remove(self._outputDBFile)
18 os.remove(self._inputDBFile)
19
20 def testFormateProfilesDB4Repet(self):
21 self._createHmmFile()
22 self._createExpectedHmmFile()
23 self._profilesDB4Repet.setInputFile(self._inputDBFile)
24 self._profilesDB4Repet.setOutputFile(self._outputDBFile)
25 self._profilesDB4Repet.run()
26 self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
27
28 def test_formateProfilesDB4Repet_GypsyDB(self):
29 self._createHmmFile_GypsyDB()
30 self._createExpectedHmmFile_GypsyDB()
31 self._profilesDB4Repet.setInputFile(self._inputDBFile)
32 self._profilesDB4Repet.setOutputFile(self._outputDBFile)
33 self._profilesDB4Repet.run()
34 self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
35
36 def _createExpectedHmmFile(self):
37 f = open(self._expectedDBFile, "w")
38 f.write("HMMER2.0 [2.3.2]\n")
39 f.write("NAME PF07582.4_AP_endonuc_2_N_APE_20.9\n")
40 f.write("ACC PF07582.4\n")
41 f.write("DESC AP endonuclease family 2 C terminus\n")
42 f.write("LENG 84\n")
43 f.write("ALPH Amino\n")
44 f.write("RF no\n")
45 f.write("CS yes\n")
46 f.write("MAP yes\n")
47 f.write("COM hmmbuild -A myhmms fn3.sto\n")
48 f.write("COM hmmcalibrate myhmms\n")
49 f.write("NSEQ 108\n")
50 f.write("DATE Thu Jan 8 17:50:26 2009\n")
51 f.write("CKSUM 6130\n")
52 f.write("GA 20.9000 20.9000;\n")
53 f.write("TC 21.2000 21.2000;\n")
54 f.write("NC 20.8000 20.8000;\n")
55 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
56 f.write("NULT -4 -8455\n")
57 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
58 f.write("EVD -45.973442 0.237545\n")
59 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
60 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
61 f.write("COM hmmcalibrate myhmms\n")
62 f.write(" -13 * -6756\n")
63 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")
64 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
65 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
66 f.write("//\n")
67 f.write("HMMER2.0 [2.3.2]\n")
68 f.write("NAME PF01606.8_Arteri_env_ENV_25.0\n")
69 f.write("ACC PF01606.8\n")
70 f.write("DESC DESC Arterivirus envelope protein\n")
71 f.write("LENG 123\n")
72 f.write("ALPH Amino\n")
73 f.write("RF no\n")
74 f.write("CS yes\n")
75 f.write("MAP yes\n")
76 f.write("COM hmmbuild -A myhmms fn3.sto\n")
77 f.write("COM hmmcalibrate myhmms\n")
78 f.write("NSEQ 108\n")
79 f.write("DATE Thu Jan 8 17:50:26 2009\n")
80 f.write("CKSUM 6130\n")
81 f.write("GA 21.0000 25.0000;\n")
82 f.write("TC 306.0000 406.0000;\n")
83 f.write("NC 10.3000 11.3000;\n")
84 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
85 f.write("NULT -4 -8455\n")
86 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
87 f.write("EVD -45.973442 0.237545\n")
88 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
89 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
90 f.write("COM hmmcalibrate myhmms\n")
91 f.write(" -13 * -6756\n")
92 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")
93 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
94 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
95 f.write("//\n")
96 f.write("HMMER2.0 [2.3.2]\n")
97 f.write("NAME PF01606.8_Dummy_name_OTHER_25.0\n")
98 f.write("ACC PF01606.8\n")
99 f.write("DESC Dummy Description\n")
100 f.write("LENG 123\n")
101 f.write("ALPH Amino\n")
102 f.write("RF no\n")
103 f.write("CS yes\n")
104 f.write("MAP yes\n")
105 f.write("COM hmmbuild -A myhmms fn3.sto\n")
106 f.write("COM hmmcalibrate myhmms\n")
107 f.write("NSEQ 108\n")
108 f.write("DATE Thu Jan 8 17:50:26 2009\n")
109 f.write("CKSUM 6130\n")
110 f.write("GA 21.0000 25.0000;\n")
111 f.write("TC 306.0000 406.0000;\n")
112 f.write("NC 10.3000 11.3000;\n")
113 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
114 f.write("NULT -4 -8455\n")
115 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
116 f.write("EVD -45.973442 0.237545\n")
117 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
118 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
119 f.write("COM hmmcalibrate myhmms\n")
120 f.write(" -13 * -6756\n")
121 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")
122 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
123 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
124 f.write("//\n")
125 f.close()
126
127 def _createHmmFile(self):
128 f = open(self._inputDBFile, "w")
129 f.write("HMMER2.0 [2.3.2]\n")
130 f.write("NAME AP_endonuc_2_N\n")
131 f.write("ACC PF07582.4\n")
132 f.write("DESC AP endonuclease family 2 C terminus\n")
133 f.write("LENG 84\n")
134 f.write("ALPH Amino\n")
135 f.write("RF no\n")
136 f.write("CS yes\n")
137 f.write("MAP yes\n")
138 f.write("COM hmmbuild -A myhmms fn3.sto\n")
139 f.write("COM hmmcalibrate myhmms\n")
140 f.write("NSEQ 108\n")
141 f.write("DATE Thu Jan 8 17:50:26 2009\n")
142 f.write("CKSUM 6130\n")
143 f.write("GA 20.9000 20.9000;\n")
144 f.write("TC 21.2000 21.2000;\n")
145 f.write("NC 20.8000 20.8000;\n")
146 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
147 f.write("NULT -4 -8455\n")
148 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
149 f.write("EVD -45.973442 0.237545\n")
150 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
151 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
152 f.write("COM hmmcalibrate myhmms\n")
153 f.write(" -13 * -6756\n")
154 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")
155 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
156 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
157 f.write("//\n")
158 f.write("HMMER2.0 [2.3.2]\n")
159 f.write("NAME Arteri_env\n")
160 f.write("ACC PF01606.8\n")
161 f.write("DESC DESC Arterivirus envelope protein\n")
162 f.write("LENG 123\n")
163 f.write("ALPH Amino\n")
164 f.write("RF no\n")
165 f.write("CS yes\n")
166 f.write("MAP yes\n")
167 f.write("COM hmmbuild -A myhmms fn3.sto\n")
168 f.write("COM hmmcalibrate myhmms\n")
169 f.write("NSEQ 108\n")
170 f.write("DATE Thu Jan 8 17:50:26 2009\n")
171 f.write("CKSUM 6130\n")
172 f.write("GA 21.0000 25.0000;\n")
173 f.write("TC 306.0000 406.0000;\n")
174 f.write("NC 10.3000 11.3000;\n")
175 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
176 f.write("NULT -4 -8455\n")
177 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
178 f.write("EVD -45.973442 0.237545\n")
179 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
180 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
181 f.write("COM hmmcalibrate myhmms\n")
182 f.write(" -13 * -6756\n")
183 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")
184 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
185 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
186 f.write("//\n")
187 f.write("HMMER2.0 [2.3.2]\n")
188 f.write("NAME Dummy_name\n")
189 f.write("ACC PF01606.8\n")
190 f.write("DESC Dummy Description\n")
191 f.write("LENG 123\n")
192 f.write("ALPH Amino\n")
193 f.write("RF no\n")
194 f.write("CS yes\n")
195 f.write("MAP yes\n")
196 f.write("COM hmmbuild -A myhmms fn3.sto\n")
197 f.write("COM hmmcalibrate myhmms\n")
198 f.write("NSEQ 108\n")
199 f.write("DATE Thu Jan 8 17:50:26 2009\n")
200 f.write("CKSUM 6130\n")
201 f.write("GA 21.0000 25.0000;\n")
202 f.write("TC 306.0000 406.0000;\n")
203 f.write("NC 10.3000 11.3000;\n")
204 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
205 f.write("NULT -4 -8455\n")
206 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
207 f.write("EVD -45.973442 0.237545\n")
208 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
209 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
210 f.write("COM hmmcalibrate myhmms\n")
211 f.write(" -13 * -6756\n")
212 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")
213 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
214 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
215 f.write("//\n")
216 f.close()
217
218 def _createExpectedHmmFile_GypsyDB(self):
219 f = open(self._expectedDBFile, "w")
220 f.write("HMMER2.0 [2.3.2]\n")
221 f.write("NAME _AP_17_6_AP_NA\n")
222 f.write("LENG 97\n")
223 f.write("ALPH Amino\n")
224 f.write("RF no\n")
225 f.write("CS no\n")
226 f.write("MAP yes\n")
227 f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
228 f.write("COM hmmcalibrate output/AP_17_6.hmm\n")
229 f.write("NSEQ 7\n")
230 f.write("DATE Tue Nov 3 12:11:06 2009\n")
231 f.write("CKSUM 7992\n")
232 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
233 f.write("NULT -4 -8455\n")
234 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
235 f.write("EVD -62.517647 0.206604\n")
236 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
237 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
238 f.write(" -193 * -2999\n")
239 f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n")
240 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
241 f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n")
242 f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n")
243 f.write("- * * * * * * * * * * * * * * * * * * * *\n")
244 f.write("- * * * * * * * * 0 \n")
245 f.write("//\n")
246 f.write("HMMER2.0 [2.3.2]\n")
247 f.write("NAME _ENV_athila_ENV_NA\n")
248 f.write("LENG 647\n")
249 f.write("ALPH Amino\n")
250 f.write("RF no\n")
251 f.write("CS no\n")
252 f.write("MAP yes\n")
253 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
254 f.write("COM hmmcalibrate ENV_athila.hmm\n")
255 f.write("NSEQ 3\n")
256 f.write("DATE Fri Sep 9 13:24:44 2005\n")
257 f.write("CKSUM 3522\n")
258 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
259 f.write("NULT -4 -8455\n")
260 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
261 f.write("EVD -12.496953 0.641902\n")
262 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
263 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
264 f.write(" -576 * -1603\n")
265 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
266 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
267 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
268 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
269 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
270 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
271 f.write("//\n")
272 f.write("HMMER2.0 [2.3.2]\n")
273 f.write("NAME _ENVathila_OTHER_NA\n")
274 f.write("LENG 647\n")
275 f.write("ALPH Amino\n")
276 f.write("RF no\n")
277 f.write("CS no\n")
278 f.write("MAP yes\n")
279 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
280 f.write("COM hmmcalibrate ENV_athila.hmm\n")
281 f.write("NSEQ 3\n")
282 f.write("DATE Fri Sep 9 13:24:44 2005\n")
283 f.write("CKSUM 3522\n")
284 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
285 f.write("NULT -4 -8455\n")
286 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
287 f.write("EVD -12.496953 0.641902\n")
288 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
289 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
290 f.write(" -576 * -1603\n")
291 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
292 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
293 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
294 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
295 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
296 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
297 f.write("//\n")
298 f.write("HMMER2.0 [2.3.2]\n")
299 f.write("NAME _MOV_cavemovirus_OTHER_NA\n")
300 f.write("LENG 302\n")
301 f.write("ALPH Amino\n")
302 f.write("RF no\n")
303 f.write("CS no\n")
304 f.write("MAP yes\n")
305 f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
306 f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n")
307 f.write("NSEQ 2\n")
308 f.write("DATE Tue Nov 3 11:25:12 2009\n")
309 f.write("CKSUM 1918\n")
310 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
311 f.write("NULT -4 -8455\n")
312 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
313 f.write("EVD -135.876633 0.154850\n")
314 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
315 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
316 f.write(" -585 * -1585\n")
317 f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n")
318 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
319 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n")
320 f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n")
321 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
322 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
323 f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n")
324 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
325 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
326 f.write("//\n")
327 f.close()
328
329 def _createHmmFile_GypsyDB(self):
330 f = open(self._inputDBFile, "w")
331 f.write("HMMER2.0 [2.3.2]\n")
332 f.write("NAME AP_17_6\n")
333 f.write("LENG 97\n")
334 f.write("ALPH Amino\n")
335 f.write("RF no\n")
336 f.write("CS no\n")
337 f.write("MAP yes\n")
338 f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
339 f.write("COM hmmcalibrate output/AP_17_6.hmm\n")
340 f.write("NSEQ 7\n")
341 f.write("DATE Tue Nov 3 12:11:06 2009\n")
342 f.write("CKSUM 7992\n")
343 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
344 f.write("NULT -4 -8455\n")
345 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
346 f.write("EVD -62.517647 0.206604\n")
347 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
348 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
349 f.write(" -193 * -2999\n")
350 f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n")
351 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
352 f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n")
353 f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n")
354 f.write("- * * * * * * * * * * * * * * * * * * * *\n")
355 f.write("- * * * * * * * * 0 \n")
356 f.write("//\n")
357 f.write("HMMER2.0 [2.3.2]\n")
358 f.write("NAME ENV_athila\n")
359 f.write("LENG 647\n")
360 f.write("ALPH Amino\n")
361 f.write("RF no\n")
362 f.write("CS no\n")
363 f.write("MAP yes\n")
364 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
365 f.write("COM hmmcalibrate ENV_athila.hmm\n")
366 f.write("NSEQ 3\n")
367 f.write("DATE Fri Sep 9 13:24:44 2005\n")
368 f.write("CKSUM 3522\n")
369 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
370 f.write("NULT -4 -8455\n")
371 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
372 f.write("EVD -12.496953 0.641902\n")
373 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
374 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
375 f.write(" -576 * -1603\n")
376 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
377 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
378 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
379 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
380 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
381 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
382 f.write("//\n")
383 f.write("HMMER2.0 [2.3.2]\n")
384 f.write("NAME ENVathila\n")
385 f.write("LENG 647\n")
386 f.write("ALPH Amino\n")
387 f.write("RF no\n")
388 f.write("CS no\n")
389 f.write("MAP yes\n")
390 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
391 f.write("COM hmmcalibrate ENV_athila.hmm\n")
392 f.write("NSEQ 3\n")
393 f.write("DATE Fri Sep 9 13:24:44 2005\n")
394 f.write("CKSUM 3522\n")
395 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
396 f.write("NULT -4 -8455\n")
397 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
398 f.write("EVD -12.496953 0.641902\n")
399 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
400 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
401 f.write(" -576 * -1603\n")
402 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
403 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
404 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
405 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
406 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
407 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
408 f.write("//\n")
409 f.write("HMMER2.0 [2.3.2]\n")
410 f.write("NAME MOV_cavemovirus\n")
411 f.write("LENG 302\n")
412 f.write("ALPH Amino\n")
413 f.write("RF no\n")
414 f.write("CS no\n")
415 f.write("MAP yes\n")
416 f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
417 f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n")
418 f.write("NSEQ 2\n")
419 f.write("DATE Tue Nov 3 11:25:12 2009\n")
420 f.write("CKSUM 1918\n")
421 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
422 f.write("NULT -4 -8455\n")
423 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
424 f.write("EVD -135.876633 0.154850\n")
425 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
426 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
427 f.write(" -585 * -1585\n")
428 f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n")
429 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
430 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n")
431 f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n")
432 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
433 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
434 f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n")
435 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
436 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
437 f.write("//\n")
438 f.close()
439
440
441 if __name__ == "__main__":
442 unittest.main()