Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_CoordsParser.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 769e306b7933 |
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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()