Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_BedParser.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 import unittest, os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from commons.core.parsing.BedParser import BedParser
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_BedParser(unittest.TestCase):
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7 def test_Parser(self):
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8 parser = BedParser("data/testBedParser1.bed")
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10 self.assertEqual(parser.getNbTranscripts(), 1)
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 for transcript in parser.getIterator():
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13 self.assertEqual(transcript.getChromosome(), "arm_X")
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14 self.assertEqual(transcript.getName(), "test1.1")
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15 self.assertEqual(transcript.getStart(), 1000)
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16 self.assertEqual(transcript.getEnd(), 2999)
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17 self.assertEqual(transcript.getDirection(), 1)
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18 self.assertEqual(transcript.getNbExons(), 2)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 exons = transcript.getExons()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 self.assertEqual(exons[0].getChromosome(), "arm_X")
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21 self.assertEqual(exons[0].getStart(), 1000)
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22 self.assertEqual(exons[0].getEnd(), 1099)
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23 self.assertEqual(exons[0].getDirection(), 1)
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24 self.assertEqual(exons[1].getChromosome(), "arm_X")
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25 self.assertEqual(exons[1].getStart(), 2000)
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26 self.assertEqual(exons[1].getEnd(), 2999)
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27 self.assertEqual(exons[1].getDirection(), 1)
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29 def test_Parser_short(self):
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30 tmpFileName = "tmpFile.bed"
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31 tmpHandle = open(tmpFileName, "w")
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32 tmpHandle.write("""X\t554748\t554904\texon
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33 X\t554748\t554904\tCDS
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34 X\t554748\t554750\tstart_codon
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35 """)
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36 tmpHandle.close()
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37 parser = BedParser(tmpFileName)
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38 self.assertEqual(parser.getNbTranscripts(), 3)
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39 for cpt, transcript in enumerate(parser.getIterator()):
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40 self.assertEqual(transcript.getNbExons(), 1)
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41 self.assertEqual(transcript.getChromosome(), "X")
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42 self.assertEqual(transcript.getStart(), 554748)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 if cpt == 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 self.assertEqual(transcript.getEnd(), 554903)
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45 self.assertEqual(transcript.getName(), "exon")
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46 elif cpt == 1:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 self.assertEqual(transcript.getEnd(), 554903)
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48 self.assertEqual(transcript.getName(), "CDS")
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49 elif cpt == 2:
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50 self.assertEqual(transcript.getEnd(), 554749)
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51 self.assertEqual(transcript.getName(), "start_codon")
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52 os.remove(tmpFileName)
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 if __name__ == '__main__':
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57 unittest.main()
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58