Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/parsing/test/Test_FastaParser.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.FastaParser import FastaParser
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2 from SMART.Java.Python.structure.Sequence import Sequence
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3 import unittest
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4
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5 class Test_FastaParser(unittest.TestCase):
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6
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7 def test_getSubsequence(self):
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8 fastaFile = "myFastaInput.fasta"
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9 self._writeInputFastaFile(fastaFile)
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10 parser = FastaParser(fastaFile)
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11 chromosome = "1"
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12 expSeq = Sequence("1:1-20 (1)", "CCTAAGCCATTGCTTGGTGA")
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13 obsSeq = parser.getSubSequence(chromosome, 1, 20, 1)
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14 self.assertEquals(expSeq, obsSeq)
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15
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16 def test_getSubsequence_long_sequence(self):
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17 fastaFile = "myFastaInput.fasta"
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18 self._writeInputFastaFile(fastaFile)
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19 parser = FastaParser(fastaFile)
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20 chromosome = "2"
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21 expSeq = Sequence("subsequence", "TGAAGA")
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22 obsSeq = parser.getSubSequence(chromosome, 55, 60, 1, "subsequence")
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23 self.assertEquals(expSeq, obsSeq)
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24
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25 def test_getSubsequence_long_sequence_inside_and_outside(self):
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26 fastaFile = "myFastaInput.fasta"
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27 self._writeInputFastaFile(fastaFile)
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28 parser = FastaParser(fastaFile)
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29 chromosome = "2"
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30 expSeq = Sequence("subsequence", "TTA")
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31 obsSeq = parser.getSubSequence(chromosome, 137, 151, 1, "subsequence")
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32 self.assertEquals(expSeq, obsSeq)
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33
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34 def test_getSubsequence_long_sequence_last_letter(self):
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35 fastaFile = "myFastaInput.fasta"
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36 self._writeInputFastaFile(fastaFile)
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37 parser = FastaParser(fastaFile)
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38 chromosome = "2"
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39 expSeq = Sequence("subsequence", "A")
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40 obsSeq = parser.getSubSequence(chromosome, 139, 151, 1, "subsequence")
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41 self.assertEquals(expSeq, obsSeq)
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42
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43 def test_getSubsequence_long_sequence_totally_outside(self):
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44 fastaFile = "myFastaInput.fasta"
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45 self._writeInputFastaFile(fastaFile)
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46 parser = FastaParser(fastaFile)
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47 chromosome = "2"
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48 isSysExit = False
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49 try:
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50 parser.getSubSequence(chromosome, 140, 151, 1, "subsequence")
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51 except:
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52 isSysExit = True
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53 self.assertTrue(isSysExit)
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54
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55 def test_setTags(self):
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56 fastaFile = "myFastaInput.fasta"
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57 self._writeInputFastaFile(fastaFile)
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58 parser = FastaParser(fastaFile)
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59 parser.setTags()
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60 expTags = {"1" : 0,
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61 "2" : 54}
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62 obsTags = parser.getTags()
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63 self.assertEquals(expTags, obsTags)
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64
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65 def _writeInputFastaFile(self, fastaFile):
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66 myHandler = open(fastaFile, 'w')
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67 myHandler.write(">1\n")
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68 myHandler.write("CCTAAGCCATTGCTTGGTGATTATGAAGGCAGTAGTCAAACCTCCACAAT\n")
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69 myHandler.write(">2\n")
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70 myHandler.write("TATGAGATCAACAGGGGCTTTGCTAGCCTGAGGGCGATTGGTCAAGGCCG\n")
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71 myHandler.write("GACCTGAAGAAATTCCTGATTGTACGTTCTGGTTACTCTTCAATTTGGGC\n")
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72 myHandler.write("TGCTTAATTATCTCCTCAATTTCAATTTGGCCATGCTTA\n")
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73
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74 if __name__ == "__main__":
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75 unittest.main()