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1 import os
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2 import unittest
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3 from commons.pyRepetUnit.profilesDB.Profiles import Profiles
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6
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7 class TestProfiles(unittest.TestCase):
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8
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9 def createInputDBFile(self):
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10 f = open(self._inputDBFile, "w")
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11 f.write("HMMER2.0 [2.3.2]\n")
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12 f.write("NAME fn3\n")
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13 f.write("ACC PF00041\n")
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14 f.write("DESC Fibronectin type III domain\n")
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15 f.write("LENG 84\n")
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16 f.write("ALPH Amino\n")
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17 f.write("RF no\n")
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18 f.write("CS yes\n")
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19 f.write("MAP yes\n")
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20 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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21 f.write("COM hmmcalibrate myhmms\n")
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22 f.write("NSEQ 108\n")
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23 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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24 f.write("CKSUM 6130\n")
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25 f.write("GA 7.8 2.0;\n")
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26 f.write("TC 7.9 2.1;\n")
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27 f.write("NC 7.0 1.1;\n")
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28 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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29 f.write("NULT -4 -8455\n")
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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")
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31 f.write("EVD -45.973442 0.237545\n")
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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")
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33 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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34 f.write("COM hmmcalibrate myhmms\n")
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35 f.write(" -13 * -6756\n")
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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")
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37 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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38 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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39 f.write("//\n")
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40 f.write("HMMER2.0 [2.3.2]\n")
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41 f.write("NAME truc\n")
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42 f.write("ACC PF00042.012\n")
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43 f.write("LENG 123\n")
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44 f.write("ALPH Amino\n")
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45 f.write("RF no\n")
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46 f.write("CS yes\n")
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47 f.write("MAP yes\n")
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48 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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49 f.write("COM hmmcalibrate myhmms\n")
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50 f.write("NSEQ 108\n")
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51 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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52 f.write("CKSUM 6130\n")
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53 f.write("GA 7.8 -1.0;\n")
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54 f.write("TC 7.9 0.1;\n")
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55 f.write("NC 7.8 0.1;\n")
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56 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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57 f.write("NULT -4 -8455\n")
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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")
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59 f.write("EVD -45.973442 0.237545\n")
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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")
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61 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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62 f.write("COM hmmcalibrate myhmms\n")
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63 f.write(" -13 * -6756\n")
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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")
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65 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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66 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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67 f.write("//\n")
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68 f.close()
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69
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70
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71 def setUp(self):
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72 self.profiles = Profiles()
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73 self._inputDBFile = "dummy.hmm"
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74
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75
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76 def testRead(self):
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77 # atomic profiles file
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78 self.createInputDBFile()
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79 file = open( self._inputDBFile )
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80 profile = self.profiles
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81 profile.read(file)
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82 self.assertEqual("fn3",profile.name)
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83 self.assertEqual("Fibronectin type III domain", profile.desc)
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84 self.assertEqual(84, profile.length)
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85 self.assertEqual("PF00041", profile.accNumber)
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86 self.assertEqual(2.0, profile.GA_cut_off)
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87 profile.read(file)
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88 self.assertEqual("truc",profile.name)
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89 self.assertEqual("", profile.desc)
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90 self.assertEqual(123, profile.length)
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91 self.assertEqual("PF00042.012", profile.accNumber)
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92 self.assertEqual(-1.0, profile.GA_cut_off)
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93 os.system("rm " + self._inputDBFile)
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94 # empty file
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95 f = open(self._inputDBFile, "w")
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96 f.close()
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97 file = open( self._inputDBFile )
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98 profile = self.profiles
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99 profile.read(file)
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100 self.assertEqual(None, profile.name)
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101 self.assertEqual(None, profile.desc)
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102 self.assertEqual(None, profile.length)
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103 self.assertEqual(None, profile.accNumber)
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104 self.assertEqual(None, profile.GA_cut_off)
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105 os.system("rm " + self._inputDBFile)
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106
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107
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108 def testReadAndRetrieve(self):
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109 # atomic profiles file
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110 self.createInputDBFile()
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111 file = open( self._inputDBFile )
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112 profile = self.profiles
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113 myProfile = profile.readAndRetrieve(file)
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114 self.assertEqual("fn3",profile.name)
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115 self.assertEqual("Fibronectin type III domain", profile.desc)
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116 self.assertEqual(84, profile.length)
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117 self.assertEqual("PF00041", profile.accNumber)
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118 self.assertEqual(2.0, profile.GA_cut_off)
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119 myProfile2 = profile.readAndRetrieve(file)
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120 self.assertEqual("truc",profile.name)
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121 self.assertEqual("", profile.desc)
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122 self.assertEqual(123, profile.length)
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123 self.assertEqual("PF00042.012", profile.accNumber)
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124 self.assertEqual(-1.0, profile.GA_cut_off)
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125 #I check if retrieve work like I want
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126 f = open("retrieveResult", "w")
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127 for item in myProfile:
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128 f.write(item)
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129 for item in myProfile2:
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130 f.write(item)
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131 f.close()
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132 self.assertTrue(FileUtils.are2FilesIdentical("retrieveResult", self._inputDBFile))
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133 os.system("rm " + self._inputDBFile)
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134 os.system("rm retrieveResult")
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135 # empty file
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136 f = open(self._inputDBFile, "w")
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137 f.close()
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138 file = open( self._inputDBFile )
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139 profile = self.profiles
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140 myProfile3 = profile.readAndRetrieve(file)
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141 self.assertEqual(None, profile.name)
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142 self.assertEqual(None, profile.desc)
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143 self.assertEqual(None, profile.length)
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144 self.assertEqual(None, profile.accNumber)
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145 self.assertEqual(None, profile.GA_cut_off)
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146 self.assertEqual(None, myProfile3)
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147 os.system("rm " + self._inputDBFile)
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148
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149
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150 if __name__ == "__main__":
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151 unittest.main() |