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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
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6 TestF_PATH = os.environ['REPET_PATH'] + '/SMART/Java/Python/TestFiles'
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7
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8
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9 class Test_F_findTss(unittest.TestCase):
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10
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11 def setUp(self):
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12 self._outputFileName = 'output.gff3'
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13 self._expOutputFileName = 'expOutput.gff3'
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14
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15 def tearDown(self):
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16 os.remove(self._outputFileName)
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17 os.remove(self._expOutputFileName)
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18
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19 def test_run_default_option(self):
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20 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -v 0" % TestF_PATH
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21 os.system(cmd)
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22 self._writeExpDefaultOption(self._expOutputFileName)
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23 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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24
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25 def test_run_normalize_option(self):
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26 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -n -v 0" % TestF_PATH
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27 os.system(cmd)
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28 self._writeExpNormalizeOption(self._expOutputFileName)
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29 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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30
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31 def test_run_distance_option(self):
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32 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -d 20 -v 0" % TestF_PATH
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33 os.system(cmd)
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34 self._writeExpDistance_option(self._expOutputFileName)
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35 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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36
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37 def test_run_colinear_option(self):
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38 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -e -v 0" % TestF_PATH
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39 os.system(cmd)
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40 self._writeExpColinearOption(self._expOutputFileName)
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41 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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42
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43 def test_run_excel_option(self):
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44 cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -c output.csv -v 0" % TestF_PATH
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45 os.system(cmd)
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46 obsCsv = 'output.csv'
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47 self.assertTrue(os.path.exists(obsCsv))
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48 os.remove(obsCsv)
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49 self._writeExpExcelOption(self._expOutputFileName)
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50 self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
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51
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52 def _writeExpDefaultOption(self, fileName):
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53 f = open(fileName, 'w')
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54 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
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55 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
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56 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
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57 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
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58 f.close()
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59
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60 def _writeExpNormalizeOption(self, fileName):
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61 f = open(fileName, 'w')
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62 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
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63 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
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64 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
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65 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
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66 f.close()
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67
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68 def _writeExpDistance_option(self, fileName):
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69 f = open(fileName, 'w')
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70 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
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71 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
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72 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
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73 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
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74 f.close()
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75
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76 def _writeExpColinearOption(self, fileName):
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77 f = open(fileName, 'w')
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78 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
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79 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
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80 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
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81 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
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82 f.close()
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83
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84 def _writeExpExcelOption(self, fileName):
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85 f = open(fileName, 'w')
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86 f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
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87 f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
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88 f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
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89 f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
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90 f.close()
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91
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92 if __name__ == "__main__":
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93 unittest.main()
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