Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/parsing/test/Test_BlatFileParser.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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() |