Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_BlatFileParser.py @ 20:c265f13066d8
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:24:43 -0400 |
parents | 769e306b7933 |
children |
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import unittest from commons.core.parsing.BlatFileParser import BlatFileParser class Test_BlatFileParser(unittest.TestCase): def test_parseBlatFile(self): fileName = "dummayBlat.psl" self._writeBlatInputFile(fileName) blatFileParser = BlatFileParser(fileName) blatFileParser.parseBlatFile() obsNbHits = len(blatFileParser.getListsOfHits()) self.assertTrue(obsNbHits == 10) obsQueries = blatFileParser.getDictOfQueries() expQueries = {'5:574_1:574_539_5:1:G/C': 1, '3:574_1:574_539_5:1:G/C': 1, '5:574_2:574_433_5:1:G/C': 1,"3:574_2:574_433_5:1:G/C":1, "5:574_5:574_607_5:1:G/C": 1, "3:574_5:574_607_5:1:G/C": 1} self.assertEquals(expQueries, obsQueries) def test_parseBlatFileByQueries(self): fileName = "dummayBlat.psl" self._writeBlatInputFile(fileName) blatFileParser = BlatFileParser(fileName) blatFileParser.parseBlatFileByQueries() obsDict = blatFileParser.getDictOfBlatHitsByQueries() obs1 = len(obsDict["5:574_1:574_539_5:1:G/C"]) obs2 = len(obsDict["3:574_1:574_539_5:1:G/C"]) obs3 = len(obsDict["5:574_2:574_433_5:1:G/C"]) obs4 = len(obsDict["3:574_2:574_433_5:1:G/C"]) obs5 = len(obsDict["5:574_5:574_607_5:1:G/C"]) obs6 = len(obsDict["3:574_5:574_607_5:1:G/C"]) self.assertTrue(obs1 == 1) self.assertTrue(obs2 == 1) self.assertTrue(obs3 == 1) self.assertTrue(obs4 == 5) self.assertTrue(obs5 == 1) self.assertTrue(obs6 == 1) obsQueries = blatFileParser.getDictOfQueries() expQueries = {'5:574_1:574_539_5:1:G/C': 1, '3:574_1:574_539_5:1:G/C': 1, '5:574_2:574_433_5:1:G/C': 1,"3:574_2:574_433_5:1:G/C":1, "5:574_5:574_607_5:1:G/C": 1, "3:574_5:574_607_5:1:G/C": 1} self.assertEquals(expQueries, obsQueries) def _writeBlatInputFile(self, fileName): file = open(fileName, "w") file.write("psLayout version 3\n") file.write("\n") file.write("match\tmis- \trep. \tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ \tQ \tQ \tQ \tT \tT \tT \tT \tblock\tblockSizes \tqStarts\t tStarts\n") file.write(" \tmatch\tmatch\t \tcount\tbases\tcount\tbases\t \tname \tsize\tstart\tend\tname \tsize\tstart\tend\tcount\n") file.write("---------------------------------------------------------------------------------------------------------------------------------------------------------------\n") file.write("246\t0\t0\t4\t0\t0\t0\t0\t-\t5:574_1:574_539_5:1:G/C\t250\t0\t250\ttaecs3B_RPH7\t3109948\t1065213\t1065463\t1\t250,\t0,\t1065213,\n") file.write("247\t0\t0\t2\t0\t0\t0\t0\t-\t3:574_1:574_539_5:1:G/C\t250\t1\t250\ttaecs3B_RPH7\t3109948\t1064962\t1065211\t1\t249,\t0,\t1064962,\n") file.write("249\t0\t0\t1\t0\t0\t0\t0\t-\t5:574_2:574_433_5:1:G/C\t250\t0\t250\ttaecs3B_RPH7\t3109948\t1065319\t1065569\t1\t250,\t0,\t1065319,\n") file.write("245\t0\t0\t5\t0\t0\t0\t0\t-\t3:574_2:574_433_5:1:G/C\t250\t0\t250\ttaecs3B_RPH8\t3109948\t1065068\t1065318\t1\t250,\t0,\t1065068,\n") file.write("247\t0\t0\t3\t0\t0\t0\t0\t-\t3:574_2:574_433_5:1:G/C\t250\t0\t250\ttaecs3B_RPH8\t3109948\t1065310\t1065560\t1\t250,\t0,\t1065310,\n") file.write("247\t0\t0\t3\t0\t0\t0\t0\t-\t3:574_2:574_433_5:1:G/C\t250\t0\t250\ttaecs3B_RPH9\t3109948\t1065059\t1065309\t1\t250,\t0,\t1065059,\n") file.write("247\t0\t0\t3\t0\t0\t0\t0\t-\t3:574_2:574_433_5:1:G/C\t250\t0\t250\ttaecs3B_RPH9\t3109948\t1064805\t1065055\t1\t250,\t0,\t1064805,\n") file.write("68\t0\t0\t1\t0\t0\t0\t0\t-\t3:574_2:574_433_5:1:G/C\t69\t0\t69\ttaecs3B_RPH9\t3109948\t1064733\t1064802\t1\t69,\t0,\t1064733,\n") file.write("245\t0\t0\t5\t0\t0\t0\t0\t-\t5:574_5:574_607_5:1:G/C\t250\t0\t250\ttaecs3B_RPH9\t3109948\t1065145\t1065395\t1\t250,\t0,\t1065145,\n") file.write("247\t0\t0\t3\t0\t0\t0\t0\t-\t3:574_5:574_607_5:1:G/C\t250\t0\t250\ttaecs3B_RPH9\t3109948\t1064894\t1065144\t1\t250,\t0,\t1064894,\n") file.close() if __name__ == "__main__": unittest.main()