Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py @ 2:7c697a8bde9f

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author yufei-luo
date Thu, 17 Jan 2013 11:02:49 -0500
parents e0f8dcca02ed
children
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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
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 from SMART.galaxy.WrappGetLetterDistribution import WrappGetLetterDistribution
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5
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6 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
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7 SMART_DATA = SMART_PATH + "/data"
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9 class Test_F_WrappGetLetterDistribution(unittest.TestCase):
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12 def setUp(self):
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13 self._dirTest = "%s/galaxy/test" % SMART_PATH
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14 self._iwrappFastq = WrappGetLetterDistribution()
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15 self._iwrappFasta = WrappGetLetterDistribution()
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16 self._expOutputCSV = "expOutputTomate.csv"
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18 def test_wrappFasta(self):
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19 self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA
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20 self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH
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21 self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH
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22 self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH
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23 self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH
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24 self._iwrappFasta._inputFileFormat = "fasta"
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25 self._iwrappFasta._csv = True
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26 if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)):
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27 self._iwrappFasta.wrapp()
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28 self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG))
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29 self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG))
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30 self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNameCSV))
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31 self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFasta._outputFileNameCSV,self._expOutputCSV))
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32 else:
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33 print "Problem : the input fasta file %s is empty!" % self._inputFileFasta
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34
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36 # def test_wrappFasta_withoutCSV_Opt(self):
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37 # self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA
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38 # self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH
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39 # self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH
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40 # self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH
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41 # self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH
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42 # self._iwrappFasta._inputFileFormat = "fasta"
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43 # self._iwrappFasta._csv = False
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44 # if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)):
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45 # self._iwrappFasta.wrapp()
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46 # self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG))
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47 # self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG))
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48 # else:
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49 # print "Problem : the input fasta file %s is empty!" % self._inputFileFasta
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50 # os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH)
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51 # os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH)
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52 #
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53 #
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54 # def test_wrappFastq(self):
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55 # self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA
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56 # self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH
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57 # self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH
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58 # self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH
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59 # self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH
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60 # self._iwrappFastq._inputFileFormat = "fastq"
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61 # self._iwrappFastq._csv = True
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62 # if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)):
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63 # self._iwrappFastq.wrapp()
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64 # self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG))
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65 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG))
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66 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNameCSV))
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67 # self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFastq._outputFileNameCSV,self._expOutputCSV))
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68 # else:
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69 # print "Problem : the input fastq file %s is empty!" % self._inputFileFastq
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70 #
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71 #
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72 # def test_wrappFastq_withoutCSV_Opt(self):
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73 # self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA
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74 # self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH
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75 # self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH
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76 # self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH
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77 # self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH
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78 # self._iwrappFastq._inputFileFormat = "fastq"
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79 # self._iwrappFastq._csv = False
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80 # if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)):
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81 # self._iwrappFastq.wrapp()
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82 # self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG))
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83 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG))
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84 # else:
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85 # print "Problem : the input fastq file %s is empty!" % self._inputFileFastq
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86 # os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH)
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87 # os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH)
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88
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89
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90 if __name__ == "__main__":
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91 unittest.main()