Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/test/Test_BlatFileParser.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 769e306b7933
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 import unittest
2 from commons.core.parsing.BlatFileParser import BlatFileParser
3
4
5 class Test_BlatFileParser(unittest.TestCase):
6
7
8 def test_parseBlatFile(self):
9 fileName = "dummayBlat.psl"
10 self._writeBlatInputFile(fileName)
11 blatFileParser = BlatFileParser(fileName)
12 blatFileParser.parseBlatFile()
13 obsNbHits = len(blatFileParser.getListsOfHits())
14 self.assertTrue(obsNbHits == 10)
15 obsQueries = blatFileParser.getDictOfQueries()
16 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}
17 self.assertEquals(expQueries, obsQueries)
18
19 def test_parseBlatFileByQueries(self):
20 fileName = "dummayBlat.psl"
21 self._writeBlatInputFile(fileName)
22 blatFileParser = BlatFileParser(fileName)
23 blatFileParser.parseBlatFileByQueries()
24 obsDict = blatFileParser.getDictOfBlatHitsByQueries()
25 obs1 = len(obsDict["5:574_1:574_539_5:1:G/C"])
26 obs2 = len(obsDict["3:574_1:574_539_5:1:G/C"])
27 obs3 = len(obsDict["5:574_2:574_433_5:1:G/C"])
28 obs4 = len(obsDict["3:574_2:574_433_5:1:G/C"])
29 obs5 = len(obsDict["5:574_5:574_607_5:1:G/C"])
30 obs6 = len(obsDict["3:574_5:574_607_5:1:G/C"])
31 self.assertTrue(obs1 == 1)
32 self.assertTrue(obs2 == 1)
33 self.assertTrue(obs3 == 1)
34 self.assertTrue(obs4 == 5)
35 self.assertTrue(obs5 == 1)
36 self.assertTrue(obs6 == 1)
37 obsQueries = blatFileParser.getDictOfQueries()
38 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}
39 self.assertEquals(expQueries, obsQueries)
40
41 def _writeBlatInputFile(self, fileName):
42 file = open(fileName, "w")
43 file.write("psLayout version 3\n")
44 file.write("\n")
45 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")
46 file.write(" \tmatch\tmatch\t \tcount\tbases\tcount\tbases\t \tname \tsize\tstart\tend\tname \tsize\tstart\tend\tcount\n")
47 file.write("---------------------------------------------------------------------------------------------------------------------------------------------------------------\n")
48 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")
49 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")
50 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")
51 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")
52 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")
53 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")
54 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")
55 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")
56 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")
57 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")
58 file.close()
59
60 if __name__ == "__main__":
61 unittest.main()