Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/test/Test_SsrParser.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_SsrParser.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,154 @@ +from commons.core.parsing.SsrParser import SsrParser +import unittest + + +class Test_SsrParser(unittest.TestCase): + + + def test_setAttributesFromString(self): + ssrLine = "MRRE1H001B07RM1\t1\t2\tta\t19\t153\t190\t734" + + iSsrParser = SsrParser() + iSsrParser.setAttributesFromString(ssrLine) + + obsBES_name = iSsrParser.getBesName() + obsBES_redundancy = iSsrParser.getBesRedundancy() + obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() + obsSSR_Motif = iSsrParser.getSsrMotif() + obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() + obsSSR_start = iSsrParser.getSsrStart() + obsSSR_end = iSsrParser.getSsrEnd() + obsBES_size = iSsrParser.getBesSize() + + expBES_name = 'MRRE1H001B07RM1' + expBES_redundancy = '1' + expSSR_nbNucleotides = '2' + expSSR_Motif = 'ta' + expSSR_Motif_number = '19' + expSSR_start = '153' + expSSR_end = '190' + expBES_size = '734' + + self.assertEquals(expBES_name, obsBES_name) + self.assertEquals(expBES_redundancy, obsBES_redundancy) + self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) + self.assertEquals(expSSR_Motif, obsSSR_Motif) + self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) + self.assertEquals(expSSR_start, obsSSR_start) + self.assertEquals(expSSR_end, obsSSR_end) + self.assertEquals(expBES_size, obsBES_size) + + def test_setAttributesFromString_empty_BESName(self): + ssrLine = "\t1\t2\tta\t19\t153\t190\t734" + + iSsrParser = SsrParser() + iSsrParser.setAttributesFromString(ssrLine) + + obsBES_name = iSsrParser.getBesName() + obsBES_redundancy = iSsrParser.getBesRedundancy() + obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() + obsSSR_Motif = iSsrParser.getSsrMotif() + obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() + obsSSR_start = iSsrParser.getSsrStart() + obsSSR_end = iSsrParser.getSsrEnd() + obsBES_size = iSsrParser.getBesSize() + + expBES_name = '' + expBES_redundancy = '' + expSSR_nbNucleotides = '' + expSSR_Motif = '' + expSSR_Motif_number = '' + expSSR_start = '' + expSSR_end = '' + expBES_size = '' + + self.assertEquals(expBES_name, obsBES_name) + self.assertEquals(expBES_redundancy, obsBES_redundancy) + self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) + self.assertEquals(expSSR_Motif, obsSSR_Motif) + self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) + self.assertEquals(expSSR_start, obsSSR_start) + self.assertEquals(expSSR_end, obsSSR_end) + self.assertEquals(expBES_size, obsBES_size) + + def test_setAttributesFromString_less_than_8_fields(self): + ssrLine = "1\t2\tta\t19\t153\t190\t734" + + iSsrParser = SsrParser() + iSsrParser.setAttributesFromString(ssrLine) + + obsBES_name = iSsrParser.getBesName() + obsBES_redundancy = iSsrParser.getBesRedundancy() + obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() + obsSSR_Motif = iSsrParser.getSsrMotif() + obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() + obsSSR_start = iSsrParser.getSsrStart() + obsSSR_end = iSsrParser.getSsrEnd() + obsBES_size = iSsrParser.getBesSize() + + expBES_name = '' + expBES_redundancy = '' + expSSR_nbNucleotides = '' + expSSR_Motif = '' + expSSR_Motif_number = '' + expSSR_start = '' + expSSR_end = '' + expBES_size = '' + + self.assertEquals(expBES_name, obsBES_name) + self.assertEquals(expBES_redundancy, obsBES_redundancy) + self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) + self.assertEquals(expSSR_Motif, obsSSR_Motif) + self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) + self.assertEquals(expSSR_start, obsSSR_start) + self.assertEquals(expSSR_end, obsSSR_end) + self.assertEquals(expBES_size, obsBES_size) + + def test_setAttributes(self): + lResults = ['MRRE1H001B07RM1','1','2','ta','19','153','190','734'] + lineNumber = 1 + + iSsrParser = SsrParser() + iSsrParser.setAttributes(lResults, lineNumber) + + obsBES_name = iSsrParser.getBesName() + obsBES_redundancy = iSsrParser.getBesRedundancy() + obsSSR_nbNucleotides = iSsrParser.getSsrNbNucleotides() + obsSSR_Motif = iSsrParser.getSsrMotif() + obsSSR_Motif_number = iSsrParser.getSsrMotifNumber() + obsSSR_start = iSsrParser.getSsrStart() + obsSSR_end = iSsrParser.getSsrEnd() + obsBES_size = iSsrParser.getBesSize() + + expBES_name = 'MRRE1H001B07RM1' + expBES_redundancy = '1' + expSSR_nbNucleotides = '2' + expSSR_Motif = 'ta' + expSSR_Motif_number = '19' + expSSR_start = '153' + expSSR_end = '190' + expBES_size = '734' + + self.assertEquals(expBES_name, obsBES_name) + self.assertEquals(expBES_redundancy, obsBES_redundancy) + self.assertEquals(expSSR_nbNucleotides, obsSSR_nbNucleotides) + self.assertEquals(expSSR_Motif, obsSSR_Motif) + self.assertEquals(expSSR_Motif_number, obsSSR_Motif_number) + self.assertEquals(expSSR_start, obsSSR_start) + self.assertEquals(expSSR_end, obsSSR_end) + self.assertEquals(expBES_size, obsBES_size) + + def test_eq_Equals(self): + SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') + SsrParser2 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') + + self.assertTrue(SsrParser1 == SsrParser2) + + def test_eq_NotEquals(self): + SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') + SsrParser2 = SsrParser('MRRE1H001A12RM3', '1', '5', 'ttta', '6', '272', '295', '852') + + self.assertFalse(SsrParser1 == SsrParser2) + +if __name__ == "__main__": + unittest.main() \ No newline at end of file