Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/writer/test/Test_Gff3Writer.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 from commons.core.writer.Gff3Writer import Gff3Writer |
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2 from SMART.Java.Python.structure.Transcript import Transcript |
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3 from SMART.Java.Python.structure.Interval import Interval |
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4 import unittest |
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5 import os |
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6 from SMART.Java.Python.misc import Utils |
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7 |
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8 class Test_Gff3Writer(unittest.TestCase): |
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9 |
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10 def test_writer(self): |
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11 obsFileName = "testGffWriter1.gff3" |
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12 writer = Gff3Writer(obsFileName) |
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13 |
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14 transcript = Transcript() |
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15 transcript.setName("test1.1") |
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16 transcript.setChromosome("arm_X") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 transcript.setStart(1000) |
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18 transcript.setEnd(4000) |
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19 transcript.setDirection("+") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 transcript.setTagValue("ID", "test1.1-1") |
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21 transcript.setTagValue("occurrence", 1) |
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22 transcript.setTagValue("nbOccurrences", 2) |
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23 |
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24 exon1 = Interval() |
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25 exon1.setChromosome("arm_X") |
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26 exon1.setStart(1000) |
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27 exon1.setEnd(2000) |
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28 exon1.setDirection("+") |
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29 |
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30 exon2 = Interval() |
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31 exon2.setChromosome("arm_X") |
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32 exon2.setStart(3000) |
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33 exon2.setEnd(4000) |
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34 exon2.setDirection("+") |
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35 |
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36 transcript.addExon(exon1) |
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37 transcript.addExon(exon2) |
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38 |
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39 writer.addTranscript(transcript) |
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40 writer.write() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 writer.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 |
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43 expFileName = "expFile.gff3" |
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44 f = open(expFileName, "w") |
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45 f.write("arm_X\tS-MART\ttranscript\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n") |
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46 f.write("arm_X\tS-MART\texon\t1000\t2000\t.\t+\t.\tID=test1.1-1-exon1;Name=test1.1-exon1;Parent=test1.1-1\n") |
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47 f.write("arm_X\tS-MART\texon\t3000\t4000\t.\t+\t.\tID=test1.1-1-exon2;Name=test1.1-exon2;Parent=test1.1-1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 f.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 |
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50 self.assertTrue(Utils.diff(expFileName, obsFileName)) |
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51 |
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52 os.remove(expFileName) |
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53 os.remove(obsFileName) |
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54 |
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55 def test_writerAltNames(self): |
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56 obsFileName = "testGffWriter1.gff3" |
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57 writer = Gff3Writer(obsFileName,title="ALTSOURCE", feature="Match", featurePart="Match-Part") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 |
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59 transcript = Transcript() |
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60 transcript.setName("test1.1") |
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61 transcript.setChromosome("arm_X") |
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62 transcript.setStart(1000) |
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63 transcript.setEnd(4000) |
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64 transcript.setDirection("+") |
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65 transcript.setTagValue("ID", "test1.1-1") |
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66 transcript.setTagValue("occurrence", 1) |
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67 transcript.setTagValue("nbOccurrences", 2) |
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68 |
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69 exon1 = Interval() |
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70 exon1.setChromosome("arm_X") |
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71 exon1.setStart(1000) |
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72 exon1.setEnd(2000) |
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73 exon1.setDirection("+") |
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74 |
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75 exon2 = Interval() |
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76 exon2.setChromosome("arm_X") |
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77 exon2.setStart(3000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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78 exon2.setEnd(4000) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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79 exon2.setDirection("+") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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80 |
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81 transcript.addExon(exon1) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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82 transcript.addExon(exon2) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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83 |
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84 writer.addTranscript(transcript) |
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85 writer.write() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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86 writer.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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87 |
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88 expFileName = "expFile.gff3" |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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89 f = open(expFileName, "w") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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90 f.write("arm_X\tALTSOURCE\tMatch\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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91 f.write("arm_X\tALTSOURCE\tMatch-Part\t1000\t2000\t.\t+\t.\tID=test1.1-1-Match-Part1;Name=test1.1-Match-Part1;Parent=test1.1-1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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92 f.write("arm_X\tALTSOURCE\tMatch-Part\t3000\t4000\t.\t+\t.\tID=test1.1-1-Match-Part2;Name=test1.1-Match-Part2;Parent=test1.1-1\n") |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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93 f.close() |
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94 |
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95 self.assertTrue(Utils.diff(expFileName, obsFileName)) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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96 |
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97 os.remove(expFileName) |
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98 os.remove(obsFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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99 |
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100 if __name__ == '__main__': |
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101 unittest.main() |