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view smart_toolShed/SMART/galaxy/test/Test_F_WrappGetLetterDistribution.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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import unittest
import os
from commons.core.utils.FileUtils import FileUtils
from SMART.galaxy.WrappGetLetterDistribution import WrappGetLetterDistribution

SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
SMART_DATA = SMART_PATH + "/data"

class Test_F_WrappGetLetterDistribution(unittest.TestCase):


    def setUp(self):
        self._dirTest = "%s/galaxy/test" % SMART_PATH
        self._iwrappFastq = WrappGetLetterDistribution()
        self._iwrappFasta = WrappGetLetterDistribution()
        self._expOutputCSV = "expOutputTomate.csv" 
       
    def test_wrappFasta(self):
        self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA
        self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH
        self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH
        self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH
        self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH
        self._iwrappFasta._inputFileFormat = "fasta"
        self._iwrappFasta._csv = True
        if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)):
            self._iwrappFasta.wrapp()
            self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG))
            self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG))    
            self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNameCSV))
            self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFasta._outputFileNameCSV,self._expOutputCSV))
        else:
            print "Problem : the input fasta file %s is empty!" % self._inputFileFasta
         
            
#    def test_wrappFasta_withoutCSV_Opt(self):
#        self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA
#        self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH
#        self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH
#        self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH
#        self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH
#        self._iwrappFasta._inputFileFormat = "fasta"
#        self._iwrappFasta._csv = False
#        if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)):
#            self._iwrappFasta.wrapp()
#            self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG))
#            self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG)) 
#        else:            
#            print "Problem : the input fasta file %s is empty!" % self._inputFileFasta
#        os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH)
#        os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH) 
#        
#                
#    def test_wrappFastq(self):
#        self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA
#        self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH
#        self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH
#        self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH
#        self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH
#        self._iwrappFastq._inputFileFormat = "fastq"
#        self._iwrappFastq._csv = True
#        if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)):
#            self._iwrappFastq.wrapp()
#            self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG))
#            self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG))    
#            self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNameCSV))
#            self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFastq._outputFileNameCSV,self._expOutputCSV))
#        else:
#            print "Problem : the input fastq file %s is empty!" % self._inputFileFastq   
#          
#        
#    def test_wrappFastq_withoutCSV_Opt(self):
#        self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA
#        self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH
#        self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH
#        self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH
#        self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH
#        self._iwrappFastq._inputFileFormat = "fastq"
#        self._iwrappFastq._csv = False
#        if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)):
#            self._iwrappFastq.wrapp()
#            self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG))
#            self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG)) 
#        else:            
#            print "Problem : the input fastq file %s is empty!" % self._inputFileFastq
#        os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH)
#        os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH)
       

if __name__ == "__main__":
    unittest.main()