Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/test/Test_MapParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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1 import unittest | |
2 import os | |
3 from commons.core.parsing.MapParser import MapParser | |
4 | |
5 class Test_MapParser(unittest.TestCase): | |
6 | |
7 | |
8 def setUp(self): | |
9 self.inputMapFileName = "testMapParser.map" | |
10 self._writeInputMapFile() | |
11 | |
12 def tearDown(self): | |
13 if os.path.exists(self.inputMapFileName): | |
14 os.remove(self.inputMapFileName) | |
15 | |
16 def test_Parser(self): | |
17 parser = MapParser(self.inputMapFileName) | |
18 | |
19 cpt = 0 | |
20 for transcript in parser.getIterator(): | |
21 cpt += 1 | |
22 if cpt == 1: | |
23 self.assertEqual(transcript.getChromosome(), "dmel_chr4") | |
24 self.assertEqual(transcript.getName(), "aagatgcgtaacggccatac_17") | |
25 self.assertEqual(transcript.getStart(), 4380) | |
26 self.assertEqual(transcript.getEnd(), 4400) | |
27 self.assertEqual(transcript.getDirection(), 1) | |
28 self.assertEqual(transcript.getSize(), 21) | |
29 elif cpt == 10: | |
30 self.assertEqual(transcript.getChromosome(), "dmel_chr4") | |
31 self.assertEqual(transcript.getName(), "aacggccatacattggtttg_12") | |
32 self.assertEqual(transcript.getStart(), 4389) | |
33 self.assertEqual(transcript.getEnd(), 4409) | |
34 self.assertEqual(transcript.getDirection(), 1) | |
35 self.assertEqual(transcript.getSize(), 21) | |
36 | |
37 | |
38 def _writeInputMapFile(self): | |
39 inputFile = open(self.inputMapFileName,'w') | |
40 inputFile.write("aagatgcgtaacggccatac_17\tdmel_chr4\t4380\t4400\n") | |
41 inputFile.write("agatgcgtaacggccataca_16\tdmel_chr4\t4381\t4401\n") | |
42 inputFile.write("gatgcgtaacggccatacat_16\tdmel_chr4\t4382\t4402\n") | |
43 inputFile.write("atgcgtaacggccatacatt_15\tdmel_chr4\t4383\t4403\n") | |
44 inputFile.write("tgcgtaacggccatacattg_15\tdmel_chr4\t4384\t4404\n") | |
45 inputFile.write("gcgtaacggccatacattgg_15\tdmel_chr4\t4385\t4405\n") | |
46 inputFile.write("cgtaacggccatacattggt_14\tdmel_chr4\t4386\t4406\n") | |
47 inputFile.write("gtaacggccatacattggtt_14\tdmel_chr4\t4387\t4407\n") | |
48 inputFile.write("taacggccatacattggttt_14\tdmel_chr4\t4388\t4408\n") | |
49 inputFile.write("aacggccatacattggtttg_12\tdmel_chr4\t4389\t4409\n") | |
50 inputFile.close() | |
51 | |
52 if __name__ == '__main__': | |
53 unittest.main() |