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1 from commons.core.utils.FileUtils import FileUtils
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2 import unittest
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3 import os
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4 import glob
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5 from commons.tools.LaunchBlaster import LaunchBlaster
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6
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7 class Test_F_LaunchBlaster(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inFileName = "DmelChr4.fa"
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11 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
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12 try:
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13 os.remove(self._inFileName)
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14 except:
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15 pass
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16 os.symlink(inFilePath, self._inFileName)
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17 self._iLaunchBlaster = LaunchBlaster(self._inFileName)
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18 self._iLaunchBlaster.setDoAllByall(True)
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19 self._iLaunchBlaster.setVerbosity(4)
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20
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21 def tearDown(self):
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22 try:
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23 FileUtils.removeFilesByPattern("%s*" % self._inFileName)
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24 os.remove("formatdb.log")
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25 except:
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26 pass
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27
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28 def test_run_as_class_1_file(self):
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29 expFileName = "%s/Tools/DmelChr4.align" % os.environ["REPET_DATA"]
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30 obsFileName = "%s.align" % self._inFileName
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31
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32 self._iLaunchBlaster.run()
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33
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34 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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35
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36 def test_run_as_class_1_file_changed_params(self):
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37 expFileName = "DmelChr4.align"
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38 with open(expFileName, "w") as fh:
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39 fh.write("dmel_chr4\t691910\t692326\tdmel_chr4\t700019\t700435\t0\t827\t100\n")
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40 obsFileName = "%s.align" % self._inFileName
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41
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42 self._iLaunchBlaster.setIdentity(100)
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43 self._iLaunchBlaster.setCPU(4)
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44 self._iLaunchBlaster.setDoClean(True)
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45 self._iLaunchBlaster.run()
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46
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47 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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48 os.remove(expFileName)
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49 self.assertTrue(glob.glob("*fa_cut*") == [])
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50 self.assertTrue(glob.glob("*Nstretch*") == [])
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51 self.assertTrue(glob.glob("*seq_treated*") == [])
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52 self.assertTrue(glob.glob("*.log") == [])
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53
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54 def test_run_as_script_1bank_1file(self):
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55 inputFileName = "chunks.fa"
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56 with open(inputFileName, "w") as f:
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57 f.write(">chunk1\n")
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58 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
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59 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
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60 expFileName = "exp.align"
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61 with open(expFileName, "w") as f:
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62 f.write("chunk1\t1\t120\tdmel_chr4\t1\t120\t2e-64\t238\t100\n")
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63 obsFileName = "%s.align" % inputFileName
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64
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65 cmd = "LaunchBlaster.py -q %s -s %s -e 0.1 -a" % (inputFileName, self._inFileName)
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66 os.system(cmd)
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67
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68 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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69 FileUtils.removeFilesByPattern("%s*" % inputFileName)
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70 os.remove(expFileName)
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71
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72 def test_run_as_script_1bank_1file_withoutABA(self):
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73 queryFileName = "chunks.fa"
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74 with open(queryFileName, "w") as f:
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75 f.write(">chunk1\n")
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76 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
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77 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
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78 subjectFileName = "genome.fa"
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79 with open(subjectFileName, "w") as f:
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80 f.write(">chunk1\n")
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81 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
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82 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
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83 f.write(">chunk2\n")
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84 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
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85 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
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86 expFileName = "exp.align"
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87 with open(expFileName, "w") as f:
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88 f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
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89 f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
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90 obsFileName = "%s.align" % queryFileName
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91
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92 cmd = "LaunchBlaster.py -q %s -s %s -e 0.1" % (queryFileName, subjectFileName)
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93 os.system(cmd)
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94
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95 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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96 FileUtils.removeFilesByPattern("%s*" % queryFileName)
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97 FileUtils.removeFilesByPattern("%s*" % subjectFileName)
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98 os.remove(expFileName)
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99
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100 if __name__ == "__main__":
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101 unittest.main() |
