Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_GffParser.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/test/Test_GffParser.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,62 @@ +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() +