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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 import shutil
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5 from commons.launcher.LaunchTallymer import LaunchTallymer
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6
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7 class Test_F_LaunchTallymer(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inFastaFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
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11
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12 def test_run_output_as_gff_cleaned(self):
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13 iLaunchTallymer = LaunchTallymer(self._inFastaFileName, clean = True, verbosity=2)
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14 iLaunchTallymer.run()
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15
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16 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
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17 obsFileName = "DmelChr4.tallymer.gff"
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18
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19 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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20 os.remove(obsFileName)
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21 os.remove("DmelChr4.tallymer.stat")
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22
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23 def test_run_with_remote_dir(self):
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24 os.makedirs("sourceDir")
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25 changedInFastaFileName = os.path.basename(self._inFastaFileName)
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26 changedInFastaFilepath = os.path.join("sourceDir",changedInFastaFileName)
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27 shutil.copy2(self._inFastaFileName, changedInFastaFilepath)
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28
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29 iLaunchTallymer = LaunchTallymer(changedInFastaFilepath, clean = True, verbosity=2)
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30 iLaunchTallymer.run()
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31
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32 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
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33 obsFileName = "DmelChr4.tallymer.gff"
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34
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35
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36 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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37 obsSourceDirFiles = os.listdir("sourceDir")
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38 expSourceDirFiles = [changedInFastaFileName,]
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39 self.assertEquals(expSourceDirFiles, obsSourceDirFiles)
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40
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41 os.remove(obsFileName)
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42 os.remove("DmelChr4.tallymer.stat")
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43 shutil.rmtree("sourceDir")
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44
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45
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46 def test_run_output_as_gff_cleaned_changed_minOccs2(self):
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47 iLaunchTallymer = LaunchTallymer(self._inFastaFileName, minOccs=2, clean = True, verbosity=2)
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48 iLaunchTallymer.run()
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49
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50 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20_minOcc2.gff" % os.environ["REPET_DATA"]
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51 obsFileName = "DmelChr4.tallymer.gff"
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52
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53 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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54 os.remove(obsFileName)
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55 os.remove("DmelChr4.tallymer.stat")
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56
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57 def test_run_output_as_gff_cleaned_relative_input(self):
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58 srcFastaFileName = self._inFastaFileName
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59 dstFastaFileName = os.path.basename(self._inFastaFileName)
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60 shutil.copy2(srcFastaFileName, dstFastaFileName)
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61 iLaunchTallymer = LaunchTallymer(dstFastaFileName, clean = True, verbosity=2)
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62 iLaunchTallymer.run()
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63
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64 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
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65 obsFileName = "DmelChr4.tallymer.gff"
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66
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67 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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68
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69 os.remove(obsFileName)
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70 os.remove("DmelChr4.tallymer.stat")
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71 os.remove(dstFastaFileName)
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72
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73 def test_run_as_script_output_as_gff_cleaned_relative_input_(self):
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74 srcFastaFileName = self._inFastaFileName
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75 dstFastaFileName = os.path.basename(self._inFastaFileName)
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76 shutil.copy2(srcFastaFileName, dstFastaFileName)
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77
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78 cmd = 'LaunchTallymer.py -i %s -s 20 -c -v 3' % (self._inFastaFileName)
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79 os.system(cmd)
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80 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.gff" % os.environ["REPET_DATA"]
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81 obsFileName = "DmelChr4.tallymer.gff"
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82
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83 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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84
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85 os.remove(obsFileName)
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86 os.remove("DmelChr4.tallymer.stat")
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87 os.remove(dstFastaFileName)
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88
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89 def test_run_output_as_wig_cleaned(self):
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90 iLaunchTallymer = LaunchTallymer(self._inFastaFileName, outputFormats="wig", clean=True)
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91 iLaunchTallymer.run()
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92
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93 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k20.wig" % os.environ["REPET_DATA"]
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94 obsFileName = "DmelChr4.tallymer.wig"
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95
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96 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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97
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98 os.remove(obsFileName)
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99 os.remove("DmelChr4.tallymer.stat")
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100
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101 def test_run_output_as_gff_and_wig_k15_cleaned(self):
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102 iLaunchTallymer = LaunchTallymer(self._inFastaFileName, merSize=15, outputFormats="wig,gff3", clean=True)
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103 iLaunchTallymer.run()
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104
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105 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
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106 obsFileName = "DmelChr4.tallymer.wig"
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107 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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108 os.remove(obsFileName)
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109
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110 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
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111 obsFileName = "DmelChr4.tallymer.gff3"
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112 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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113 os.remove(obsFileName)
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114
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115 os.remove("DmelChr4.tallymer.stat")
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116
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117 def test_run_as_script_run_output_as_gff_and_wig_k15_cleaned(self):
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118 logFileName = "test.log"
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119 cmd = 'LaunchTallymer.py -i %s -s 15 -f gff,wig,vero -c -v 3 > %s' % (self._inFastaFileName, logFileName)
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120 os.system(cmd)
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121
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122 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.wig" % os.environ["REPET_DATA"]
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123 obsFileName = "DmelChr4.tallymer.wig"
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124 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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125 os.remove(obsFileName)
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126
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127 expFileName = "%s/Tools/DmelChr4.fa.tallymer_k15.gff3" % os.environ["REPET_DATA"]
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128 obsFileName = "DmelChr4.tallymer.gff"
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129 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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130 os.remove(obsFileName)
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131
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132 expLogFileName = "exp.log"
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133 with open(expLogFileName, "w") as f:
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134 f.write(" LaunchTallymer - WARNING - Warning: ignoring invalid formats: <vero>\n")
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135 f.write(" LaunchTallymer - INFO - Starting to run tallymer search of sequence DmelChr4.fa \n")
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136 f.write(" LaunchTallymer - INFO - Finished running tallymer scan of sequence DmelChr4.fa \n")
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137 f.write(" LaunchTallymer - INFO - Starting to run tallymer search to map conversion\n")
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138 f.write(" LaunchTallymer - INFO - Finished tallymer search to map conversion\n")
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139 f.write(" LaunchTallymer - INFO - Generating wig file\n")
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140 f.write(" LaunchTallymer - INFO - Generating gff file\n")
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141 obsLogFileName = "obs.log"
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142 os.system("cut -d'-' -f4,5,6 %s > %s" % (logFileName, obsLogFileName))
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143 self.assertTrue(FileUtils.are2FilesIdentical(expLogFileName, obsLogFileName))
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144
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145 os.remove(logFileName)
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146 os.remove(expLogFileName)
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147 os.remove(obsLogFileName)
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148 os.remove("DmelChr4.tallymer.stat")
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149
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150 if __name__ == "__main__":
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151 unittest.main() |
