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1 import unittest
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2 import os, glob
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3 from SMART.Java.Python.getWigProfile import GetWigProfile
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4
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5
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6 class Test_F_GetWigProfile(unittest.TestCase):
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7
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8 def setUp(self):
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9 self.transcriptFileName = "transcriptFile.gff3"
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10 self.wigFileName = "file.wig"
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11 self.outputFileName = "outputFile.png"
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12
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13 def tearDown(self):
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14 for fileRoot in (self.transcriptFileName, self.wigFileName, 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 .RData .chr1.index ")
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18
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19 def test_run_simple(self):
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20 handle = open(self.transcriptFileName, "w")
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21 handle.write("chr1\tSMART\tmRNA\t10\t20\t.\t+\t.\tID=test1;Name=test1")
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22 handle.close()
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23 handle = open(self.wigFileName, "w")
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24 handle.write("variableStep chrom=chr1\n")
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25 handle.write("1 1\n")
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26 handle.write("2 1\n")
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27 handle.write("3 1\n")
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28 handle.write("4 1\n")
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29 handle.write("5 1\n")
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30 handle.write("6 1\n")
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31 handle.write("7 1\n")
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32 handle.write("8 1\n")
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33 handle.write("9 1\n")
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34 handle.write("10 1\n")
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35 handle.write("11 2\n")
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36 handle.write("12 3\n")
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37 handle.write("13 4\n")
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38 handle.write("14 5\n")
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39 handle.write("15 5\n")
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40 handle.write("16 5\n")
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41 handle.write("17 5\n")
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42 handle.write("18 5\n")
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43 handle.write("19 5\n")
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44 handle.write("20 5\n")
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45 handle.write("21 1\n")
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46 handle.write("21 1\n")
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47 handle.close()
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48 wigProfile = GetWigProfile(0)
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49 wigProfile.strands = False
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50 wigProfile.inputFileName = self.transcriptFileName
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51 wigProfile.inputFormat = "gff3"
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52 wigProfile.wig = self.wigFileName
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53 wigProfile.nbPoints = 11
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54 wigProfile.distance = 1
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55 wigProfile.smoothenForce = None
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56 wigProfile.log = False
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57 wigProfile.outputFileName = self.outputFileName
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58 wigProfile.readTranscripts()
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59 wigProfile.smoothen()
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60 wigProfile.plot()
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61 self.assertTrue(os.path.exists(self.outputFileName))
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62
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63 if __name__ == "__main__":
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64 unittest.main()
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65
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