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1 from commons.core.sql.DbFactory import DbFactory
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2 from commons.core.utils.FileUtils import FileUtils
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3 import subprocess
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4 import os
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5 import unittest
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6 from commons.tools.AlignTEOnGenomeAccordingToAnnotation import AlignTEOnGenomeAccordingToAnnotation
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7
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8 class Test_F_AlignTEOnGenomeAccordingToAnnotation(unittest.TestCase):
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9
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10 def test_run_merge_same_paths(self):
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11 pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
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12 queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
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13 subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
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14 pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
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15 queryTableName = "testDmelChr4_chr_seq"
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16 subjectTableName = "testDmelChr4_refTEs_seq"
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17 iDb = DbFactory.createInstance()
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18 iDb.createTable(queryTableName, "seq", queryFileName, True)
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19 iDb.createTable(subjectTableName, "seq", subjectFileName, True)
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20 iDb.createTable(pathTableName, "path", pathFileName, True)
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21 expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
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22
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23 iATOGATA = AlignTEOnGenomeAccordingToAnnotation(pathTableName, queryTableName, subjectTableName, True)
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24 iATOGATA.run()
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25 obsFileName = "obs%s_merge.alignedSeq" % pathTableName
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26 iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
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27
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28 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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29
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30 os.remove(obsFileName)
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31 iDb.dropTable(queryTableName)
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32 iDb.dropTable(subjectTableName)
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33 iDb.dropTable(pathTableName)
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34 iDb.dropTable("%s_align" % pathTableName)
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35 iDb.close()
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36
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37 def test_run_as_script_merge_same_paths(self):
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38 pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
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39 queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
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40 subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
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41 pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
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42 queryTableName = "testDmelChr4_chr_seq"
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43 subjectTableName = "testDmelChr4_refTEs_seq"
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44 iDb = DbFactory.createInstance()
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45 iDb.createTable(queryTableName, "seq", queryFileName, True)
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46 iDb.createTable(subjectTableName, "seq", subjectFileName, True)
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47 iDb.createTable(pathTableName, "path", pathFileName, True)
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48 expFileName = "%s/Tools/exp%s_merge.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
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49
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50 cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s -m " % (pathTableName, queryTableName, subjectTableName)
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51 process = subprocess.Popen(cmd, shell = True)
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52 process.communicate()
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53 obsFileName = "obs%s_merge.alignedSeq" % pathTableName
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54 iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
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55
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56 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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57
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58 os.remove(obsFileName)
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59 iDb.dropTable(queryTableName)
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60 iDb.dropTable(subjectTableName)
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61 iDb.dropTable(pathTableName)
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62 iDb.dropTable("%s_align" % pathTableName)
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63 iDb.close()
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64
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65 def test_run_as_script_without_merge(self):
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66 pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
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67 queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
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68 subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
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69 pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
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70 queryTableName = "testDmelChr4_chr_seq"
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71 subjectTableName = "testDmelChr4_refTEs_seq"
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72 iDb = DbFactory.createInstance()
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73 iDb.createTable(queryTableName, "seq", queryFileName, True)
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74 iDb.createTable(subjectTableName, "seq", subjectFileName, True)
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75 iDb.createTable(pathTableName, "path", pathFileName, True)
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76 expFileName = "%s/Tools/exp%s.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
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77
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78 cmd = "AlignTEOnGenomeAccordingToAnnotation.py -p %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName)
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79 process = subprocess.Popen(cmd, shell = True)
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80 process.communicate()
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81 obsFileName = "obs%s.alignedSeq" % pathTableName
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82 iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
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83
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84 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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85
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86 os.remove(obsFileName)
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87 iDb.dropTable(queryTableName)
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88 iDb.dropTable(subjectTableName)
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89 iDb.dropTable(pathTableName)
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90 iDb.dropTable("%s_align" % pathTableName)
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91 iDb.close()
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92
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93 # def test_run_as_script_merge_same_paths_old(self):
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94 # pathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
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95 # queryFileName = "%s/commons/DmelChr4.fa" % os.environ["REPET_DATA"]
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96 # subjectFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
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97 # pathTableName = "testDmelChr4_chr_allTEs_nr_noSSR_join_path"
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98 # queryTableName = "testDmelChr4_chr_seq"
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99 # subjectTableName = "testDmelChr4_refTEs_seq"
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100 # iDb = DbFactory.createInstance()
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101 # iDb.createTable(queryTableName, "seq", queryFileName, True)
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102 # iDb.createTable(subjectTableName, "seq", subjectFileName, True)
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103 # iDb.createTable(pathTableName, "path", pathFileName, True)
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104 # expFileName = "%s/Tools/exp%s_merge_old.alignedSeq" % (os.environ["REPET_DATA"], pathTableName)
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105 #
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106 # cmd = "srptAlignPath.py -m %s -q %s -s %s" % (pathTableName, queryTableName, subjectTableName)
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107 # process = subprocess.Popen(cmd, shell = True)
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108 # process.communicate()
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109 # obsFileName = "obs%s.alignedSeq" % pathTableName
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110 # iDb.exportDataToFile("%s_align" % pathTableName, obsFileName)
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111 #
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112 # self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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113 #
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114 # os.remove(obsFileName)
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115 # iDb.dropTable(queryTableName)
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116 # iDb.dropTable(subjectTableName)
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117 # iDb.dropTable(pathTableName)
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118 # iDb.dropTable("%s_align" % pathTableName)
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119 # iDb.close()
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120 #
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121 if __name__ == "__main__":
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122 unittest.main() |
