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1 import unittest
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2 import os
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3 from commons.pyRepetUnit.profilesDB.Profiles import Profiles
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4 from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils
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5
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6
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7 class TestProfilesDatabankUtils( unittest.TestCase ):
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8
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9 def setUp( self ):
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10 self.profilesDBUtils = ProfilesDatabankUtils()
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11
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12
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13 def test_read_emptyFile( self ):
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14 file = open( "pfamDBEmpty", "w" )
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15 file.close()
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16 pfamDB2 = self.profilesDBUtils.read( "pfamDBEmpty" )
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17 self.assertEquals( None, pfamDB2 )
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18 os.remove( "pfamDBEmpty" )
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19
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20
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21 def test_read( self ):
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22 f = open("dummy.hmm", "w")
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23 f.write("HMMER2.0 [2.3.2]\n")
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24 f.write("NAME fn3\n")
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25 f.write("ACC PF00041\n")
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26 f.write("DESC Fibronectin type III domain\n")
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27 f.write("LENG 84\n")
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28 f.write("ALPH Amino\n")
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29 f.write("RF no\n")
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30 f.write("CS yes\n")
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31 f.write("MAP yes\n")
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32 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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33 f.write("COM hmmcalibrate myhmms\n")
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34 f.write("NSEQ 108\n")
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35 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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36 f.write("CKSUM 6130\n")
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37 f.write("GA 7.8 -1.0\n")
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38 f.write("TC 7.9 0.1\n")
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39 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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40 f.write("NULT -4 -8455\n")
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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")
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42 f.write("EVD -45.973442 0.237545\n")
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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")
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44 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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45 f.write("COM hmmcalibrate myhmms\n")
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46 f.write(" -13 * -6756\n")
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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")
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48 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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49 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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50 f.write("//\n")
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51 f.write("HMMER2.0 [2.3.2]\n")
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52 f.write("NAME truc\n")
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53 f.write("ACC PF00041\n")
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54 f.write("LENG 123\n")
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55 f.write("ALPH Amino\n")
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56 f.write("RF no\n")
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57 f.write("CS yes\n")
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58 f.write("MAP yes\n")
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59 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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60 f.write("COM hmmcalibrate myhmms\n")
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61 f.write("NSEQ 108\n")
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62 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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63 f.write("CKSUM 6130\n")
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64 f.write("GA 7.8 -1.0\n")
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65 f.write("TC 7.9 0.1\n")
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66 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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67 f.write("NULT -4 -8455\n")
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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")
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69 f.write("EVD -45.973442 0.237545\n")
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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")
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71 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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72 f.write("COM hmmcalibrate myhmms\n")
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73 f.write(" -13 * -6756\n")
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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")
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75 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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76 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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77 f.write("//\n")
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78 f.close()
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79 pfamDB = self.profilesDBUtils.read("dummy.hmm")
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80 expectedProfiles1 = Profiles()
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81 expectedProfiles1.name = "fn3"
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82 expectedProfiles1.desc = "Fibronectin type III domain"
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83 expectedProfiles1.length = 84
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84 expectedProfiles2 = Profiles()
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85 expectedProfiles2.name = "truc"
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86 expectedProfiles2.desc = ""
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87 expectedProfiles2.length = 123
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88
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89 self.assertEqual( expectedProfiles1.name, pfamDB.get(0).name )
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90 self.assertEqual( expectedProfiles1.desc, pfamDB.get(0).desc )
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91 self.assertEqual( expectedProfiles1.length, pfamDB.get(0).length )
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92 self.assertEqual( expectedProfiles2.name, pfamDB.get(1).name )
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93 self.assertEqual( expectedProfiles2.desc, pfamDB.get(1).desc )
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94 self.assertEqual( expectedProfiles2.length, pfamDB.get(1).length )
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95
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96 os.remove("dummy.hmm")
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97
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98
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99 if __name__ == "__main__":
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100 unittest.main()
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101 |
