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1 import unittest, os, os.path
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2 from SMART.Java.Python.misc import Utils
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3 from SMART.Java.Python.ClusterizeByTags import ClusterizeByTags
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4
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5 class Test_F_ClusterizeByTags(unittest.TestCase):
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6
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7 def setUp(self):
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8 self._inputFileName = "inputFileTest.gff3"
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9 self._expOutputFileName = "expOutput.gff3"
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10 self._outputFileName = "output.gff3"
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11
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12 def tearDown(self):
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13 for file in (self._inputFileName, self._expOutputFileName, self._outputFileName):
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14 if os.path.exists(file):
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15 os.remove(file)
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16
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17 def test_diff_simple(self):
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18 handle = open(self._inputFileName, "w")
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19 handle.write("""chr1\tS-MART\ttest1.1\t100\t200\t.\t+\t.\tName=test1.1;score=10;ID=test1.1
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20 chr1\tS-MART\ttest1.2\t300\t400\t.\t+\t.\tName=test1.2;score=15;ID=test1.2
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21 chr1\tS-MART\ttest1.3\t500\t600\t.\t+\t.\tName=test1.3;score=15;ID=test1.3
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22 chr1\tS-MART\ttest1.4\t700\t800\t.\t+\t.\tName=test1.4;score=100;ID=test1.4
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23 chr1\tS-MART\ttest1.5\t900\t1000\t.\t+\t.\tName=test1.5;score=110;ID=test1.5
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24 chr1\tS-MART\ttest1.6\t1100\t1200\t.\t+\t.\tName=test1.6;score=105;ID=test1.6
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25 """)
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26 handle.close()
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27 handle = open(self._expOutputFileName, "w")
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28 handle.write("""chr1 S-MART test1.1 100 600 40 + . nbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3
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29 chr1 S-MART exon 100 200 10 + . ID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1
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30 chr1 S-MART exon 300 400 15 + . ID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1
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31 chr1 S-MART exon 500 600 15 + . ID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1
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32 chr1 S-MART test1.4 700 1200 315 + . nbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6
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33 chr1 S-MART exon 700 800 100 + . ID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4
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34 chr1 S-MART exon 900 1000 110 + . ID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4
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35 chr1 S-MART exon 1100 1200 105 + . ID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4
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36 """)
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37 handle.close()
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38 cbt = ClusterizeByTags(0)
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39 cbt.setInputFile(self._inputFileName, "gff3")
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40 cbt.setOutputFile(self._outputFileName)
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41 cbt.setTag("score", None)
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42 cbt.setThreshold(20)
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43 cbt.setOperation("diff")
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44 cbt.setMaxDistance(None)
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45 cbt.run()
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46 self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))
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47
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48 def test_diff_two_strands(self):
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49 handle = open(self._inputFileName, "w")
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50 handle.write("""chr1\tS-MART\ttest1.1\t100\t200\t.\t+\t.\tName=test1.1;score=10;ID=test1.1
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51 chr1\tS-MART\ttest1.2\t300\t400\t.\t+\t.\tName=test1.2;score=15;ID=test1.2
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52 chr1\tS-MART\ttest1.3\t500\t600\t.\t+\t.\tName=test1.3;score=15;ID=test1.3
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53 chr1\tS-MART\ttest1.4\t700\t800\t.\t-\t.\tName=test1.4;score=10;ID=test1.4
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54 chr1\tS-MART\ttest1.5\t900\t1000\t.\t-\t.\tName=test1.5;score=15;ID=test1.5
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55 chr1\tS-MART\ttest1.6\t1100\t1200\t.\t-\t.\tName=test1.6;score=15;ID=test1.6
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56 """)
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57 handle.close()
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58 handle = open(self._expOutputFileName, "w")
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59 handle.write("""chr1 S-MART test1.4 700 1200 40 - . nbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6
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60 chr1 S-MART exon 700 800 10 - . ID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4
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61 chr1 S-MART exon 900 1000 15 - . ID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4
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62 chr1 S-MART exon 1100 1200 15 - . ID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4
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63 chr1 S-MART test1.1 100 600 40 + . nbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3
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64 chr1 S-MART exon 100 200 10 + . ID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1
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65 chr1 S-MART exon 300 400 15 + . ID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1
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66 chr1 S-MART exon 500 600 15 + . ID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1
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67 """)
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68 handle.close()
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69 cbt = ClusterizeByTags(0)
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70 cbt.setInputFile(self._inputFileName, "gff3")
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71 cbt.setOutputFile(self._outputFileName)
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72 cbt.setTag("score", None)
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73 cbt.setThreshold(20)
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74 cbt.setOperation("diff")
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75 cbt.setMaxDistance(None)
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76 cbt.run()
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77 self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))
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78
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79 def test_diff_one_strands(self):
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80 handle = open(self._inputFileName, "w")
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81 handle.write("""chr1\tS-MART\ttest1.1\t100\t200\t.\t+\t.\tName=test1.1;score=10;ID=test1.1
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82 chr1\tS-MART\ttest1.2\t300\t400\t.\t+\t.\tName=test1.2;score=15;ID=test1.2
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83 chr1\tS-MART\ttest1.3\t500\t600\t.\t+\t.\tName=test1.3;score=15;ID=test1.3
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84 chr1\tS-MART\ttest1.4\t700\t800\t.\t-\t.\tName=test1.4;score=10;ID=test1.4
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85 chr1\tS-MART\ttest1.5\t900\t1000\t.\t-\t.\tName=test1.5;score=15;ID=test1.5
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86 chr1\tS-MART\ttest1.6\t1100\t1200\t.\t-\t.\tName=test1.6;score=15;ID=test1.6
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87 """)
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88 handle.close()
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89 handle = open(self._expOutputFileName, "w")
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90 handle.write("""chr1 S-MART test1.1 100 600 40 + . nbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3
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91 chr1 S-MART exon 100 200 10 + . ID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1
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92 chr1 S-MART exon 300 400 15 + . ID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1
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93 chr1 S-MART exon 500 600 15 + . ID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1
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94 chr1 S-MART test1.4 700 1200 40 - . nbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6
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95 chr1 S-MART exon 700 800 10 - . ID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4
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96 chr1 S-MART exon 900 1000 15 - . ID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4
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97 chr1 S-MART exon 1100 1200 15 - . ID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4
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98 """)
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99 handle.close()
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100 cbt = ClusterizeByTags(0)
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101 cbt.setInputFile(self._inputFileName, "gff3")
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102 cbt.setOutputFile(self._outputFileName)
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103 cbt.setTag("score", None)
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104 cbt.setThreshold(20)
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105 cbt.setOperation("diff")
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106 cbt.setMaxDistance(None)
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107 cbt.setOneStrand(True)
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108 cbt.run()
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109 self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))
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110
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111 def test_diff_distance(self):
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112 handle = open(self._inputFileName, "w")
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113 handle.write("""chr1\tS-MART\ttest1.1\t100\t200\t.\t+\t.\tName=test1.1;score=10;ID=test1.1
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114 chr1\tS-MART\ttest1.2\t300\t400\t.\t+\t.\tName=test1.2;score=15;ID=test1.2
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115 chr1\tS-MART\ttest1.3\t500\t600\t.\t+\t.\tName=test1.3;score=15;ID=test1.3
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116 chr1\tS-MART\ttest1.4\t1000\t1100\t.\t+\t.\tName=test1.4;score=10;ID=test1.4
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117 chr1\tS-MART\ttest1.5\t1200\t1300\t.\t+\t.\tName=test1.5;score=15;ID=test1.5
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118 chr1\tS-MART\ttest1.6\t1400\t1500\t.\t+\t.\tName=test1.6;score=15;ID=test1.6
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119 """)
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120 handle.close()
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121 handle = open(self._expOutputFileName, "w")
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122 handle.write("""chr1 S-MART test1.1 100 600 40 + . nbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3
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123 chr1 S-MART exon 100 200 10 + . ID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1
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124 chr1 S-MART exon 300 400 15 + . ID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1
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125 chr1 S-MART exon 500 600 15 + . ID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1
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126 chr1 S-MART test1.4 1000 1500 40 + . nbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6
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127 chr1 S-MART exon 1000 1100 10 + . ID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4
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128 chr1 S-MART exon 1200 1300 15 + . ID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4
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129 chr1 S-MART exon 1400 1500 15 + . ID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4
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130 """)
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131 handle.close()
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132 cbt = ClusterizeByTags(0)
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133 cbt.setInputFile(self._inputFileName, "gff3")
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134 cbt.setOutputFile(self._outputFileName)
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135 cbt.setTag("score", None)
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136 cbt.setThreshold(20)
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137 cbt.setOperation("diff")
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138 cbt.setMaxDistance(200)
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139 cbt.run()
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140 self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))
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141
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142
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143 if __name__ == "__main__":
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144 unittest.main()
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