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1 import unittest
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2 import os, os.path
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3 from SMART.Java.Python.misc import Utils
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4
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5 SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
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6
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7 class Test_F_compareOverlapping(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inputFileQuery = "inputFileTest1.bed"
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11 self._inputFileReference = "inputFileTest2.bed"
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12 self._inputFileName3 = "inputFileTest3.bed"
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13 self._expOutputFileName = "expOutput.gff3"
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14 self._outputFileName = "output.gff3"
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15 self._writeInputFileQuery()
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16 self._writeInputFileRefence()
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17 self._writeInputFile3()
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18
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19 def tearDown(self):
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20 for fileName in (self._inputFileQuery, self._inputFileReference, self._inputFileName3, self._expOutputFileName, self._outputFileName):
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21 if os.path.exists(fileName):
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22 os.remove(fileName)
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23
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24 def test_runAsScript_withoutOption(self):
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25 self._writeOutputFile_withoutOption(self._expOutputFileName)
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26 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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27 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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28
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29 def test_runAsScript_optionNFirstNucleotide(self):
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30 self._writeOutputFile_NFirstNucleotide(self._expOutputFileName)
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31 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -S 200 -s 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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32 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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33
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34 def test_runAsScript_optionNLastNucleotide(self):
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35 self._writeOutputFile_NLastNucleotide(self._expOutputFileName)
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36 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -U 200 -u 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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37 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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38
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39 def test_runAsScript_option_5PrimeExtension(self):
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40 self._writeOutputFile_5PrimeExtension(self._expOutputFileName)
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41 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -E 110 -e 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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42 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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43
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44 def test_runAsScript_option_3PrimeExtension(self):
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45 self._writeOutputFile_3PrimeExtension(self._expOutputFileName)
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46 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -N 110 -n 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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47 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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48
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49 def test_runAsScript_colinear(self):
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50 self._writeOutputFile_colinear(self._expOutputFileName)
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51 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -c -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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52 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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53
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54 def test_runAsScript_antisense(self):
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55 self._writeOutputFile_antisense(self._expOutputFileName)
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56 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -a -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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57 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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58
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59 def test_runAsScript_minOverlap(self):
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60 self._writeOutputFile_minOverlap(self._expOutputFileName)
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61 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -m 51 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
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62 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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63
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64 def test_runAsScript_pcOverlap(self):
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65 self._writeOutputFile_pcOverlap(self._expOutputFileName)
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66 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -p 60 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileName3, self._outputFileName))
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67 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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68
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69 def test_runAsScript_included(self):
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70 self._writeOutputFile_included(self._expOutputFileName)
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71 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -k -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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72 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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73
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74 def test_runAsScript_including(self):
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75 self._writeOutputFile_including(self._expOutputFileName)
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76 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -K -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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77 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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78
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79 def test_runAsScript_includeNotOverlap(self):
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80 self._writeOutputFile_includeNotOverlap(self._expOutputFileName)
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81 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -O -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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82 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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83
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84 def test_runAsScript_exclude(self):
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85 self._writeOutputFile_exclude(self._expOutputFileName)
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86 os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -x -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))
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87 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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88
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89 def _writeInputFileQuery(self):
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90 f = open(self._inputFileQuery, "w")
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91 f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
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92 f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
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93 f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
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94 f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t1\t3100,\t0,\n")
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95 f.close()
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96
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97 def _writeInputFileRefence(self):
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98 f = open(self._inputFileReference, "w")
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99 f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
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100 f.close()
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101
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102 def _writeInputFile3(self):
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103 f = open(self._inputFileName3, "w")
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104 f.write("arm_X\t1000\t2000\ttest2.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
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105 f.write("arm_X\t250\t350\ttest2.2\t1000\t+\t250\t350\t0\t1\t100,\t0,\n")
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106 f.write("arm_X\t150\t250\ttest2.3\t1000\t+\t150\t250\t0\t1\t100,\t0,\n")
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107 f.close()
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108
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109 def _writeOutputFile_withoutOption(self, outputFileName):
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110 f = open(outputFileName, "w")
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111 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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112 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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113 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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114 f.close()
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115
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116 def _writeOutputFile_NFirstNucleotide(self, outputFileName):
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117 f = open(outputFileName, "w")
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118 f.write("arm_X\tS-MART\ttranscript\t1000\t1199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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119 f.close()
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120
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121 def _writeOutputFile_NLastNucleotide(self, outputFileName):
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122 f = open(outputFileName, "w")
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123 f.write("arm_X\tS-MART\ttranscript\t1800\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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124 f.close()
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125
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126 def _writeOutputFile_5PrimeExtension(self, outputFileName):
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127 f = open(outputFileName, "w")
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128 f.write("arm_X\tS-MART\ttranscript\t0\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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129 f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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130 f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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131 f.close()
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132
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133 def _writeOutputFile_3PrimeExtension(self, outputFileName):
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134 f = open(outputFileName, "w")
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135 f.write("arm_X\tS-MART\ttranscript\t100\t3309\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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136 f.write("arm_X\tS-MART\ttranscript\t1000\t2109\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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137 f.write("arm_X\tS-MART\ttranscript\t890\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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138 f.close()
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139
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140 def _writeOutputFile_colinear(self, outputFileName):
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141 f = open(outputFileName, "w")
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142 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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143 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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144 f.close()
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145
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146 def _writeOutputFile_antisense(self, outputFileName):
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147 f = open(outputFileName, "w")
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148 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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149 f.close()
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150
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151 def _writeOutputFile_minOverlap(self, outputFileName):
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152 f = open(outputFileName, "w")
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153 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.3,test2.2,test2.1;nbOverlaps=3.000000;ID=test1.4;Name=test1.4\n")
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154 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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155 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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156 f.close()
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157
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158 def _writeOutputFile_pcOverlap(self, outputFileName):
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159 f = open(outputFileName, "w")
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160 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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161 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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162 f.close()
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163
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164 def _writeOutputFile_includeNotOverlap(self, outputFileName):
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165 f = open(outputFileName, "w")
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166 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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167 f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tnbOverlaps=0;ID=test1.3;Name=test1.3\n")
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168 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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169 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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170 f.close()
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171
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172 def _writeOutputFile_exclude(self, outputFileName):
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173 f = open(outputFileName, "w")
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174 f.write("arm_X\tS-MART\ttranscript\t100\t199\t.\t+\t.\tID=test1.3;Name=test1.3\n")
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175 f.close()
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176
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177 def _writeOutputFile_included(self, outputFileName):
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178 f = open(outputFileName, "w")
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179 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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180 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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181 f.close()
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182
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183 def _writeOutputFile_including(self, outputFileName):
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184 f = open(outputFileName, "w")
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185 f.write("arm_X\tS-MART\ttranscript\t100\t3199\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\n")
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186 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t+\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\n")
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187 f.write("arm_X\tS-MART\ttranscript\t1000\t1999\t.\t-\t.\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\n")
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188 f.close()
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189
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190 def _writeInputFileQuery_withExon(self):
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191 f = open(self._inputFileQuery, "w")
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192 f.write("arm_X\t1000\t2000\ttest1.1\t1000\t+\t1000\t2000\t0\t1\t1000,\t0,\n")
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193 f.write("arm_X\t1000\t2000\ttest1.2\t1000\t-\t1000\t2000\t0\t1\t1000,\t0,\n")
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194 f.write("arm_X\t100\t200\ttest1.3\t1000\t+\t100\t200\t0\t1\t100,\t0,\n")
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195 f.write("arm_X\t100\t3200\ttest1.4\t1000\t+\t100\t3200\t0\t2\t100,100,\t0,3000,\n")
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196 f.close()
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197
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198 if __name__ == "__main__":
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199 unittest.main()
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