Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_GffParser.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
---|---|
date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
children |
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import unittest from commons.core.parsing.GffParser import GffParser class Test_GffParser(unittest.TestCase): def test_Parser(self): parser = GffParser("data/testGffParser1.gff3") self.assertEqual(parser.getNbTranscripts(), 3) cpt = 0 for transcript in parser.getIterator(): cpt += 1 if cpt == 1: self.assertEqual(transcript.getChromosome(), "arm_X") self.assertEqual(transcript.getName(), "test1") self.assertEqual(transcript.getStart(), 1000) self.assertEqual(transcript.getEnd(), 2000) self.assertEqual(transcript.getDirection(), 1) self.assertEqual(transcript.getNbExons(), 1) self.assertEqual(transcript.getTagValue("field"), "value1") exons = transcript.getExons() self.assertEqual(exons[0].getChromosome(), "arm_X") self.assertEqual(exons[0].getStart(), 1000) self.assertEqual(exons[0].getEnd(), 2000) self.assertEqual(exons[0].getDirection(), 1) self.assertEqual(transcript.getSize(), 1001) elif cpt == 2: self.assertEqual(transcript.getChromosome(), "arm_X") self.assertEqual(transcript.getName(), "test2") self.assertEqual(transcript.getStart(), 10000) self.assertEqual(transcript.getEnd(), 20000) self.assertEqual(transcript.getDirection(), -1) self.assertEqual(transcript.getNbExons(), 2) self.assertEqual(transcript.getTagValue("field"), "value2") exons = transcript.getExons() self.assertEqual(exons[0].getChromosome(), "arm_X") self.assertEqual(exons[0].getStart(), 10000) self.assertEqual(exons[0].getEnd(), 10100) self.assertEqual(exons[0].getDirection(), -1) self.assertEqual(transcript.getSize(), 9602) if cpt == 3: self.assertEqual(transcript.getChromosome(), "arm_X") self.assertEqual(transcript.getName(), "test1.1") self.assertEqual(transcript.getStart(), 1000) self.assertEqual(transcript.getEnd(), 2000) self.assertEqual(transcript.getDirection(), 1) self.assertEqual(transcript.getNbExons(), 1) self.assertEqual(transcript.getTagValue("ID"), "test1.1-1") exons = transcript.getExons() self.assertEqual(exons[0].getChromosome(), "arm_X") self.assertEqual(exons[0].getStart(), 1000) self.assertEqual(exons[0].getEnd(), 2000) self.assertEqual(exons[0].getDirection(), 1) self.assertEqual(transcript.getSize(), 1001) if __name__ == '__main__': unittest.main()