Mercurial > repos > yufei-luo > s_mart
annotate 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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from commons.core.parsing.BlatFileParser import BlatFileParser |
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3 |
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4 |
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5 class Test_BlatFileParser(unittest.TestCase): |
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6 |
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7 |
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8 def test_parseBlatFile(self): |
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9 fileName = "dummayBlat.psl" |
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10 self._writeBlatInputFile(fileName) |
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11 blatFileParser = BlatFileParser(fileName) |
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12 blatFileParser.parseBlatFile() |
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13 obsNbHits = len(blatFileParser.getListsOfHits()) |
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14 self.assertTrue(obsNbHits == 10) |
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15 obsQueries = blatFileParser.getDictOfQueries() |
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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} |
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17 self.assertEquals(expQueries, obsQueries) |
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18 |
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19 def test_parseBlatFileByQueries(self): |
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20 fileName = "dummayBlat.psl" |
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21 self._writeBlatInputFile(fileName) |
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22 blatFileParser = BlatFileParser(fileName) |
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23 blatFileParser.parseBlatFileByQueries() |
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24 obsDict = blatFileParser.getDictOfBlatHitsByQueries() |
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25 obs1 = len(obsDict["5:574_1:574_539_5:1:G/C"]) |
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26 obs2 = len(obsDict["3:574_1:574_539_5:1:G/C"]) |
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27 obs3 = len(obsDict["5:574_2:574_433_5:1:G/C"]) |
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28 obs4 = len(obsDict["3:574_2:574_433_5:1:G/C"]) |
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29 obs5 = len(obsDict["5:574_5:574_607_5:1:G/C"]) |
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30 obs6 = len(obsDict["3:574_5:574_607_5:1:G/C"]) |
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31 self.assertTrue(obs1 == 1) |
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32 self.assertTrue(obs2 == 1) |
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33 self.assertTrue(obs3 == 1) |
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34 self.assertTrue(obs4 == 5) |
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35 self.assertTrue(obs5 == 1) |
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36 self.assertTrue(obs6 == 1) |
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37 obsQueries = blatFileParser.getDictOfQueries() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 self.assertEquals(expQueries, obsQueries) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 |
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41 def _writeBlatInputFile(self, fileName): |
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42 file = open(fileName, "w") |
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43 file.write("psLayout version 3\n") |
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44 file.write("\n") |
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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") |
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46 file.write(" \tmatch\tmatch\t \tcount\tbases\tcount\tbases\t \tname \tsize\tstart\tend\tname \tsize\tstart\tend\tcount\n") |
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47 file.write("---------------------------------------------------------------------------------------------------------------------------------------------------------------\n") |
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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") |
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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") |
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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") |
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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") |
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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") |
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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") |
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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") |
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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") |
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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") |
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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") |
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58 file.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 |
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60 if __name__ == "__main__": |
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61 unittest.main() |