Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_BowtieParser.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 from commons.core.parsing.BowtieParser import BowtieParser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import unittest, os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 class Test_BlatParser(unittest.TestCase):
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8 def test_simple(self):
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9 fileName = "tmpFile.bowtie"
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10 handle = open(fileName, "w")
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11 handle.write("HWI-EAS179_0053:2:1:1365:7879#0/2\t+\tchrXHet\t191698\tACCGCTGAACCACTTTCATNCNTGGGATTGTGAACTGAAACTGTTCACATGAACTTGGAATTCCCAGTAAGTGTGA\tLcaYcacLaTdd`dacacYBaBTa^^TL^M`]`^aa`Tca`LaLTUa]a_bcLcTMMMMa^a^`bT`ccT_UbM_B\t0\t19:G>N,21:T>N\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 handle.write("HWI-EAS179_0053:2:1:1365:7879#0/1\t-\tchrXHet\t191803\tCCCCTTGTACACACCGCCCGTCGCTACTACCGATTGAATTATGTAGTGAGGTCTCCGGACGTGATCACTGTGACGC\tBBBBBBBBB`O`DS]]aYabaaa[ULYLY]^b`^a^aZZZ_LLLca_a_b^^aYdbd``d^ccaY`_caccc^acc\t0\t33:T>G,72:T>C\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 handle.write("HWI-EAS179_0053:2:1:1371:11420#0/2\t+\tchr3L\t16569206\tTATGAGCGCCAATTTTGCANTTTTATTTTTGTACAAGCCAAGGGTTTTGCAACATTCACAGCGCTTGCCACTTGTC\tcY^bcYLcaL]`]]`aaTaBaab^_ZZ__R[`[cYccc^Ybb^_L`L`Y`aM_a_TcTcc`LL]]MYaYabbTY`^\t0\t19:G>N\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 handle.write("HWI-EAS179_0053:2:1:1371:11420#0/1\t-\tchr3L\t16569298\tAATGAACCATTGTAATTACCCACAACACATACAGTCACACACGAGATGCACACAAGTCGGAAACGGAAGCGAGACG\tBBBBBBBBBBBBBBBBBBBBBB^T`]Y^`KZY__LY_a]^T^ccYaYY__YT]VZbL]`b^cLT^a^caccYbT^b\t0\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 handle.close()
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16
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17 parser = BowtieParser("tmpFile.bowtie", 0)
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18 for cpt, mapping in enumerate(parser.getIterator()):
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19 transcript = mapping.getTranscript()
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20 if cpt == 0:
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21 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/2")
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22 self.assertEquals(transcript.getChromosome(), "chrXHet")
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23 self.assertEquals(transcript.getDirection(), 1)
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24 self.assertEquals(transcript.getStart(), 191699)
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25 self.assertEquals(transcript.getEnd(), 191774)
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26 self.assertEquals(transcript.getTagValue("nbMismatches"), 2)
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27 elif cpt == 1:
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28 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1365:7879#0/1")
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29 self.assertEquals(transcript.getChromosome(), "chrXHet")
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30 self.assertEquals(transcript.getDirection(), -1)
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31 self.assertEquals(transcript.getStart(), 191804)
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32 self.assertEquals(transcript.getEnd(), 191879)
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33 self.assertEquals(transcript.getTagValue("nbMismatches"), 2)
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34 elif cpt == 2:
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35 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/2")
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36 self.assertEquals(transcript.getChromosome(), "chr3L")
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37 self.assertEquals(transcript.getDirection(), 1)
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38 self.assertEquals(transcript.getStart(), 16569207)
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39 self.assertEquals(transcript.getEnd(), 16569282)
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40 self.assertEquals(transcript.getTagValue("nbMismatches"), 1)
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41 elif cpt == 3:
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42 self.assertEquals(transcript.getName(), "HWI-EAS179_0053:2:1:1371:11420#0/1")
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43 self.assertEquals(transcript.getChromosome(), "chr3L")
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44 self.assertEquals(transcript.getDirection(), -1)
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45 self.assertEquals(transcript.getStart(), 16569299)
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46 self.assertEquals(transcript.getEnd(), 16569374)
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47 self.assertEquals(transcript.getTagValue("nbMismatches"), 0)
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48 else:
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49 self.fail()
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50
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51 os.remove(fileName)
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55 if __name__ == "__main__":
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56 unittest.main()
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57