コード例 #1
0
ファイル: bioioTest.py プロジェクト: Nikaidolab/mafTools
 def testFastaReadWriteC(self):
     """Tests consistency with C version of this function.
     """
     tempFile = getTempFile()
     self.tempFiles.append(tempFile)
     tempFile2 = getTempFile()
     self.tempFiles.append(tempFile2)
     for test in xrange(0, self.testNo):
         fastaNumber = random.choice(xrange(10))
         l = [ getRandomSequence() for i in xrange(fastaNumber) ]
         fileHandle = open(tempFile, 'w')
         for name, seq in l:
             fastaWrite(fileHandle, name, seq)
         fileHandle.close()
         
         command = "sonLib_fastaCTest %s %s" % (tempFile, tempFile2)
         
         print command
         
         system(command)
         
         fileHandle = open(tempFile2, 'r')
         l.reverse()
         for i in fastaRead(fileHandle):
             name, seq = i
             assert i == l.pop()
             fastaWrite(sys.stdout, name, seq)
         fileHandle.close()
コード例 #2
0
ファイル: bioioTest.py プロジェクト: Nikaidolab/mafTools
 def testFastaReadWrite(self):
     tempFile = getTempFile()
     self.tempFiles.append(tempFile)
     for test in xrange(0, self.testNo):
         fastaNumber = random.choice(xrange(10))
         l = [ getRandomSequence() for i in xrange(fastaNumber) ]
         fileHandle = open(tempFile, 'w')
         for name, seq in l:
             fastaWrite(fileHandle, name, seq)
         fileHandle.close()
         fileHandle = open(tempFile, 'r')
         l.reverse()
         for i in fastaRead(fileHandle):
             assert i == l.pop()
             name, seq = i
             fastaWrite(sys.stdout, name, seq)
         fileHandle.close()
コード例 #3
0
ファイル: bioioTest.py プロジェクト: Nikaidolab/mafTools
 def testFastqReadWrite(self):
     tempFile = getTempFile()
     self.tempFiles.append(tempFile)
     for test in xrange(0, self.testNo):
         fastaNumber = random.choice(xrange(10))
         fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in xrange(fastaNumber) ]]
         fH = open(tempFile, 'w')
         for name, seq, quals in fastqs:
             fastqWrite(fH, name, seq, quals)
         fH.close()
         fastqs.reverse()
         for i in fastqRead(tempFile):
             assert i == fastqs.pop()
             name, seq, quals = i
             fastqWrite(sys.stdout, name, seq, quals)