Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_plotCoverage.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import unittest
2 import os, glob
3 from SMART.Java.Python.plotCoverage import PlotParser
4
5
6 class Test_F_PlotCoverage(unittest.TestCase):
7
8 def setUp(self):
9 self.queryFileName = "queryFile.gff3"
10 self.refFileName = "refFile.gff3"
11 self.outputFileName = "outputFile"
12
13 def tearDown(self):
14 for fileRoot in (self.queryFileName, self.refFileName, self.outputFileName):
15 for file in glob.glob("%s*" % (fileRoot)):
16 os.remove(file)
17 os.remove(".RData")
18
19 def test_run_simple(self):
20 handle = open(self.refFileName, "w")
21 handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1")
22 handle.close()
23 handle = open(self.queryFileName, "w")
24 handle.write("chr1\tSMART\tmRNA\t1100\t1200\t.\t+\t.\tID=test2.1;Name=test2.1\n")
25 handle.write("chr1\tSMART\tmRNA\t1300\t1400\t.\t+\t.\tID=test2.2;Name=test2.2\n")
26 handle.close()
27 pp = PlotParser(0)
28 pp.addInput(0, self.queryFileName, "gff3")
29 pp.addInput(1, self.refFileName, "gff3")
30 pp.setLabels("x", "y")
31 pp.setPlotSize(1000, 500)
32 pp.setOutput(self.outputFileName)
33 pp.start()
34 self.assertTrue(os.path.exists("%s_test1_overlap.png" % (self.outputFileName)))
35 self.assertTrue(os.path.exists("%s_test1_coverage.png" % (self.outputFileName)))
36
37 if __name__ == "__main__":
38 unittest.main()
39