Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/profilesDB/tests/Test_ProfilesDB4Repet.py @ 31:0ab839023fe4
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
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import unittest import os from commons.pyRepetUnit.profilesDB.ProfilesDB4Repet import ProfilesDB4Repet from commons.core.utils.FileUtils import FileUtils class Test_ProfilesDB4Repet(unittest.TestCase): def setUp(self): self._inputDBFile = "./datas/dummy.hmm" self._expectedDBFile = "./datas/expected.hmm" self._outputDBFile = "./datas/output.hmm" self._profilesDB4Repet = ProfilesDB4Repet() def tearDown(self): os.remove(self._expectedDBFile) os.remove(self._outputDBFile) os.remove(self._inputDBFile) def testFormateProfilesDB4Repet(self): self._createHmmFile() self._createExpectedHmmFile() self._profilesDB4Repet.setInputFile(self._inputDBFile) self._profilesDB4Repet.setOutputFile(self._outputDBFile) self._profilesDB4Repet.run() self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile)) def test_formateProfilesDB4Repet_GypsyDB(self): self._createHmmFile_GypsyDB() self._createExpectedHmmFile_GypsyDB() self._profilesDB4Repet.setInputFile(self._inputDBFile) self._profilesDB4Repet.setOutputFile(self._outputDBFile) self._profilesDB4Repet.run() self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile)) def _createExpectedHmmFile(self): f = open(self._expectedDBFile, "w") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME PF07582.4_AP_endonuc_2_N_APE_20.9\n") f.write("ACC PF07582.4\n") f.write("DESC AP endonuclease family 2 C terminus\n") f.write("LENG 84\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 20.9000 20.9000;\n") f.write("TC 21.2000 21.2000;\n") f.write("NC 20.8000 20.8000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME PF01606.8_Arteri_env_ENV_25.0\n") f.write("ACC PF01606.8\n") f.write("DESC DESC Arterivirus envelope protein\n") f.write("LENG 123\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 21.0000 25.0000;\n") f.write("TC 306.0000 406.0000;\n") f.write("NC 10.3000 11.3000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME PF01606.8_Dummy_name_OTHER_25.0\n") f.write("ACC PF01606.8\n") f.write("DESC Dummy Description\n") f.write("LENG 123\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 21.0000 25.0000;\n") f.write("TC 306.0000 406.0000;\n") f.write("NC 10.3000 11.3000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.close() def _createHmmFile(self): f = open(self._inputDBFile, "w") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME AP_endonuc_2_N\n") f.write("ACC PF07582.4\n") f.write("DESC AP endonuclease family 2 C terminus\n") f.write("LENG 84\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 20.9000 20.9000;\n") f.write("TC 21.2000 21.2000;\n") f.write("NC 20.8000 20.8000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME Arteri_env\n") f.write("ACC PF01606.8\n") f.write("DESC DESC Arterivirus envelope protein\n") f.write("LENG 123\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 21.0000 25.0000;\n") f.write("TC 306.0000 406.0000;\n") f.write("NC 10.3000 11.3000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME Dummy_name\n") f.write("ACC PF01606.8\n") f.write("DESC Dummy Description\n") f.write("LENG 123\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS yes\n") f.write("MAP yes\n") f.write("COM hmmbuild -A myhmms fn3.sto\n") f.write("COM hmmcalibrate myhmms\n") f.write("NSEQ 108\n") f.write("DATE Thu Jan 8 17:50:26 2009\n") f.write("CKSUM 6130\n") f.write("GA 21.0000 25.0000;\n") f.write("TC 306.0000 406.0000;\n") f.write("NC 10.3000 11.3000;\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n") f.write("EVD -45.973442 0.237545\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write("COM hmmcalibrate myhmms\n") f.write(" -13 * -6756\n") 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") f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n") f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n") f.write("//\n") f.close() def _createExpectedHmmFile_GypsyDB(self): f = open(self._expectedDBFile, "w") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME _AP_17_6_AP_NA\n") f.write("LENG 97\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n") f.write("COM hmmcalibrate output/AP_17_6.hmm\n") f.write("NSEQ 7\n") f.write("DATE Tue Nov 3 12:11:06 2009\n") f.write("CKSUM 7992\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -62.517647 0.206604\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -193 * -2999\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n") 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") f.write("- * * * * * * * * * * * * * * * * * * * *\n") f.write("- * * * * * * * * 0 \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME _ENV_athila_ENV_NA\n") f.write("LENG 647\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") f.write("COM hmmcalibrate ENV_athila.hmm\n") f.write("NSEQ 3\n") f.write("DATE Fri Sep 9 13:24:44 2005\n") f.write("CKSUM 3522\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -12.496953 0.641902\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -576 * -1603\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME _ENVathila_OTHER_NA\n") f.write("LENG 647\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") f.write("COM hmmcalibrate ENV_athila.hmm\n") f.write("NSEQ 3\n") f.write("DATE Fri Sep 9 13:24:44 2005\n") f.write("CKSUM 3522\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -12.496953 0.641902\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -576 * -1603\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME _MOV_cavemovirus_OTHER_NA\n") f.write("LENG 302\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n") f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n") f.write("NSEQ 2\n") f.write("DATE Tue Nov 3 11:25:12 2009\n") f.write("CKSUM 1918\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -135.876633 0.154850\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -585 * -1585\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") f.write("//\n") f.close() def _createHmmFile_GypsyDB(self): f = open(self._inputDBFile, "w") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME AP_17_6\n") f.write("LENG 97\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n") f.write("COM hmmcalibrate output/AP_17_6.hmm\n") f.write("NSEQ 7\n") f.write("DATE Tue Nov 3 12:11:06 2009\n") f.write("CKSUM 7992\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -62.517647 0.206604\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -193 * -2999\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n") 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") f.write("- * * * * * * * * * * * * * * * * * * * *\n") f.write("- * * * * * * * * 0 \n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME ENV_athila\n") f.write("LENG 647\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") f.write("COM hmmcalibrate ENV_athila.hmm\n") f.write("NSEQ 3\n") f.write("DATE Fri Sep 9 13:24:44 2005\n") f.write("CKSUM 3522\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -12.496953 0.641902\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -576 * -1603\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME ENVathila\n") f.write("LENG 647\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n") f.write("COM hmmcalibrate ENV_athila.hmm\n") f.write("NSEQ 3\n") f.write("DATE Fri Sep 9 13:24:44 2005\n") f.write("CKSUM 3522\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -12.496953 0.641902\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -576 * -1603\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n") f.write("//\n") f.write("HMMER2.0 [2.3.2]\n") f.write("NAME MOV_cavemovirus\n") f.write("LENG 302\n") f.write("ALPH Amino\n") f.write("RF no\n") f.write("CS no\n") f.write("MAP yes\n") f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n") f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n") f.write("NSEQ 2\n") f.write("DATE Tue Nov 3 11:25:12 2009\n") f.write("CKSUM 1918\n") f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n") f.write("NULT -4 -8455\n") f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n") f.write("EVD -135.876633 0.154850\n") f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n") f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n") f.write(" -585 * -1585\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") 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") f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n") f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n") f.write("//\n") f.close() if __name__ == "__main__": unittest.main()