Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_CoordsParser.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_CoordsParser.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,105 @@ +import unittest +from commons.core.parsing.CoordsParser import CoordsParser +from SMART.Java.Python.mappingToCoordinates import MappingToCoordinates + + +class Test_CoordsParser(unittest.TestCase): + + + def test_Parser(self): + parser = CoordsParser("data/testCoordsParser.coords") + + cpt = 0 + for mapping in parser.getIterator(): + transcript = mapping.getTranscript() + cpt += 1 + if cpt == 1: + self.assertEqual(transcript.getChromosome(), "scaffold_1") + self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") + self.assertEqual(transcript.getStart(), 1) + self.assertEqual(transcript.getEnd(), 6251) + self.assertEqual(transcript.getDirection(), -1) + self.assertEqual(transcript.getNbExons(), 1) + self.assertEqual(transcript.getTagValue("identity"), 89.030000000000001) + exons = transcript.getExons() + self.assertEqual(exons[0].getChromosome(), "scaffold_1") + self.assertEqual(exons[0].getStart(), 1) + self.assertEqual(exons[0].getEnd(), 6251) + self.assertEqual(exons[0].getDirection(), -1) + self.assertEqual(transcript.getSize(), 6251) + elif cpt == 2: + self.assertEqual(transcript.getChromosome(), "scaffold_1") + self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") + self.assertEqual(transcript.getStart(), 9127) + self.assertEqual(transcript.getEnd(), 11947) + self.assertEqual(transcript.getDirection(), -1) + self.assertEqual(transcript.getNbExons(), 1) + self.assertEqual(transcript.getTagValue("identity"), 90.450000000000003) + exons = transcript.getExons() + self.assertEqual(exons[0].getChromosome(), "scaffold_1") + self.assertEqual(exons[0].getStart(), 9127) + self.assertEqual(exons[0].getEnd(), 11947) + self.assertEqual(exons[0].getDirection(), -1) + self.assertEqual(transcript.getSize(), 2821) + if cpt == 3: + self.assertEqual(transcript.getChromosome(), "scaffold_1") + self.assertEqual(transcript.getName(), "gi|240254421:1-30427671") + self.assertEqual(transcript.getStart(), 12201) + self.assertEqual(transcript.getEnd(), 12953) + self.assertEqual(transcript.getDirection(), -1) + self.assertEqual(transcript.getNbExons(), 1) + exons = transcript.getExons() + self.assertEqual(exons[0].getChromosome(), "scaffold_1") + self.assertEqual(exons[0].getStart(), 12201) + self.assertEqual(exons[0].getEnd(), 12953) + self.assertEqual(exons[0].getDirection(), -1) + self.assertEqual(transcript.getSize(), 753) + + def test_Parser_showcoord(self): + parser = CoordsParser("data/testCoordsParser_showcoord.coords") + expTranscriptCount = 1 + obsTranscriptCount = 0 + + for mapping in parser.getIterator(): + transcript = mapping.getTranscript() + obsTranscriptCount += 1 + self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001") + self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003") + self.assertEqual(transcript.getStart(), 296) + self.assertEqual(transcript.getEnd(), 2292) + self.assertEqual(transcript.getDirection(), 1) + self.assertEqual(transcript.getTagValue("identity"), 98.30) + self.assertEqual(transcript.getTagValue("target_pident"), 98.30) + self.assertEqual(transcript.getTagValue("target_pcover"), 3.32) + self.assertEqual(transcript.getTagValue("target_length"), 60273) + self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 1 2001") + self.assertEqual(transcript.getSize(), 1997) + + self.assertEquals(expTranscriptCount, obsTranscriptCount) + + def test_Parser_showcoord_promer(self): + parser = CoordsParser("data/testCoordsParser_showcoord_promer.coords") + expTranscriptCount = 1 + obsTranscriptCount = 0 + + for mapping in parser.getIterator(): + transcript = mapping.getTranscript() + obsTranscriptCount += 1 + self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001") + self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003") + self.assertEqual(transcript.getStart(), 291) + self.assertEqual(transcript.getEnd(), 1229) + self.assertEqual(transcript.getDirection(), -1) + self.assertEqual(transcript.getTagValue("identity"), 94.25) + self.assertEqual(transcript.getTagValue("target_pident"), 94.25) + self.assertEqual(transcript.getTagValue("target_pcover"), 1.56) + self.assertEqual(transcript.getTagValue("target_length"), 60273) + self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 939 1") + self.assertEqual(transcript.getSize(), 939) + + self.assertEquals(expTranscriptCount, obsTranscriptCount) + + +if __name__ == '__main__': + unittest.main() +