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1 import unittest
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2 import os, glob
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3 from SMART.Java.Python.mapperAnalyzer import MapperAnalyzer
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4 from commons.core.parsing.GffParser import GffParser
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5
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6 class Test_F_mapperAnalyzer(unittest.TestCase):
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7
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8 def setUp(self):
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9 self.readsFileName = "inputFile.fastq"
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10 self.mappingFileName = "inputFile.sam"
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11 self.outputFileName = "outputFile.gff3"
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12
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13 def tearDown(self):
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14 for fileRoot in (self.readsFileName, self.mappingFileName, self.outputFileName):
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15 for file in glob.glob("%s*" % (fileRoot)):
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16 os.remove(file)
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17 os.system("rm tmpNames_* tmpSequences_* smartdb*")
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18
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19 def test_run_simple(self):
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20 handle = open(self.readsFileName, "w")
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21 handle.write("@read1\n")
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22 handle.write("AAAAAAAAAAAAAAAAAAAA\n")
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23 handle.write("+\n")
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24 handle.write("AAAAAAAAAAAAAAAAAAAA\n")
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25 handle.write("@read2\n")
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26 handle.write("CCCCCCCCCCCCCCCCCCCC\n")
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27 handle.write("+\n")
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28 handle.write("AAAAAAAAAAAAAAAAAAAA\n")
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29 handle.close()
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30 handle = open(self.mappingFileName, "w")
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31 handle.write("read1\t0\tchr1\t1\t30\t20M\t*\t0\t0\tAAAAAAAAAAAAAAAAAAAA\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
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32 handle.write("read2\t0\tchr2\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
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33 handle.write("read2\t0\tchr3\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
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34 handle.close()
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35 analyzer = MapperAnalyzer(0)
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36 analyzer.setMappingFile(self.mappingFileName, "sam")
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37 analyzer.setSequenceFile(self.readsFileName, "fastq")
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38 analyzer.setOutputFile(self.outputFileName, "S-MART")
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39 analyzer.setMaxMappings(1)
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40 analyzer.mergeExons(True)
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41 analyzer.analyze()
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42
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43 parser = GffParser(self.outputFileName)
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44 self.assertEqual(parser.getNbTranscripts(), 1)
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45 for transcript in parser.getIterator():
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46 self.assertEqual(transcript.getName(), "read1")
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47 self.assertEqual(transcript.getChromosome(), "chr1")
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48 self.assertEqual(transcript.getStart(), 1)
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49 self.assertEqual(transcript.getEnd(), 20)
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50 self.assertEqual(transcript.getDirection(), 1)
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51
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52
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53 if __name__ == "__main__":
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54 unittest.main()
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55
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