|
18
|
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
|
