Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_MapParser.py @ 14:c79b9ae3f65f
Deleted selected files
author | m-zytnicki |
---|---|
date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
import unittest import os from commons.core.parsing.MapParser import MapParser class Test_MapParser(unittest.TestCase): def setUp(self): self.inputMapFileName = "testMapParser.map" self._writeInputMapFile() def tearDown(self): if os.path.exists(self.inputMapFileName): os.remove(self.inputMapFileName) def test_Parser(self): parser = MapParser(self.inputMapFileName) cpt = 0 for transcript in parser.getIterator(): cpt += 1 if cpt == 1: self.assertEqual(transcript.getChromosome(), "dmel_chr4") self.assertEqual(transcript.getName(), "aagatgcgtaacggccatac_17") self.assertEqual(transcript.getStart(), 4380) self.assertEqual(transcript.getEnd(), 4400) self.assertEqual(transcript.getDirection(), 1) self.assertEqual(transcript.getSize(), 21) elif cpt == 10: self.assertEqual(transcript.getChromosome(), "dmel_chr4") self.assertEqual(transcript.getName(), "aacggccatacattggtttg_12") self.assertEqual(transcript.getStart(), 4389) self.assertEqual(transcript.getEnd(), 4409) self.assertEqual(transcript.getDirection(), 1) self.assertEqual(transcript.getSize(), 21) def _writeInputMapFile(self): inputFile = open(self.inputMapFileName,'w') inputFile.write("aagatgcgtaacggccatac_17\tdmel_chr4\t4380\t4400\n") inputFile.write("agatgcgtaacggccataca_16\tdmel_chr4\t4381\t4401\n") inputFile.write("gatgcgtaacggccatacat_16\tdmel_chr4\t4382\t4402\n") inputFile.write("atgcgtaacggccatacatt_15\tdmel_chr4\t4383\t4403\n") inputFile.write("tgcgtaacggccatacattg_15\tdmel_chr4\t4384\t4404\n") inputFile.write("gcgtaacggccatacattgg_15\tdmel_chr4\t4385\t4405\n") inputFile.write("cgtaacggccatacattggt_14\tdmel_chr4\t4386\t4406\n") inputFile.write("gtaacggccatacattggtt_14\tdmel_chr4\t4387\t4407\n") inputFile.write("taacggccatacattggttt_14\tdmel_chr4\t4388\t4408\n") inputFile.write("aacggccatacattggtttg_12\tdmel_chr4\t4389\t4409\n") inputFile.close() if __name__ == '__main__': unittest.main()