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1 import unittest
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2 import os
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3 from commons.core.parsing.GffParser import GffParser
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4 from SMART.Java.Python.getRandomRegions import RandomRegionsGenerator
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5
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6 MIN_SIZE = 36
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7 MAX_SIZE = 100
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8 CHR = "chr1"
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9 CHR_SIZE = 1000000
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10 NB_READS = 1000
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11
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12 class Test_F_getRandomRegions(unittest.TestCase):
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13
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14 def setUp(self):
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15 self._outputFileName = 'output.gff3'
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16
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17 def tearDown(self):
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18 for fileName in [self._outputFileName]:
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19 if os.path.exists(fileName):
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20 os.remove(fileName)
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21
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22 def test_simple(self):
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23 iRR = RandomRegionsGenerator(0)
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24 iRR.setMinSize(MIN_SIZE)
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25 iRR.setMaxSize(MAX_SIZE)
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26 iRR.setGenomeSize(CHR_SIZE)
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27 iRR.setChromosomeName(CHR)
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28 iRR.setStrands(False)
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29 iRR.setNumber(NB_READS)
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30 iRR.setOutputFile(self._outputFileName)
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31 iRR.run()
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32 parser = GffParser(self._outputFileName, 0)
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33 starts = set()
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34 self.assertTrue(parser.getNbTranscripts(), CHR_SIZE)
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35 for transcript in parser.getIterator():
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36 start = transcript.getStart()
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37 end = transcript.getEnd()
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38 size = transcript.getSize()
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39 chromosome = transcript.getChromosome()
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40 strand = transcript.getDirection()
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41 self.assertTrue(start not in starts)
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42 self.assertTrue(start >= 1)
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43 self.assertTrue(end <= CHR_SIZE)
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44 self.assertEquals(chromosome, CHR)
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45 self.assertEquals(strand, 1)
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46 starts.add(start)
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47
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48 def test_both_strands(self):
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49 iRR = RandomRegionsGenerator(0)
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50 iRR.setMinSize(MIN_SIZE)
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51 iRR.setMaxSize(MAX_SIZE)
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52 iRR.setGenomeSize(CHR_SIZE)
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53 iRR.setChromosomeName(CHR)
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54 iRR.setStrands(True)
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55 iRR.setNumber(NB_READS)
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56 iRR.setOutputFile(self._outputFileName)
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57 iRR.run()
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58 parser = GffParser(self._outputFileName, 0)
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59 strands = set()
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60 for transcript in parser.getIterator():
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61 strands.add(transcript.getDirection())
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62 self.assertTrue(1 in strands)
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63 self.assertTrue(-1 in strands)
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64
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65 if __name__ == "__main__":
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66 unittest.main()
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