Example #1
0
 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()
def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("--unmasked")
    parser.add_argument("--hardmasked")
    parser.add_argument("--softmasked")

    options = parser.parse_args()

    unmasked = open(options.unmasked, 'r')
    hardmasked = open(options.hardmasked, 'r')
    softmasked = open(options.softmasked, 'w')

    for unmaskedInfo, hardmaskedInfo in itertools.izip(bioio.fastaRead(unmasked), bioio.fastaRead(hardmasked)):
        unmaskedName, unmaskedSeq = unmaskedInfo
        hardmaskedName, hardmaskedSeq = hardmaskedInfo
        print("processing sequence: %s" % unmaskedName)
        assert unmaskedName == hardmaskedName

        softmaskedSeq = ''
        for unmaskedBase, hardmaskedBase in zip(unmaskedSeq, hardmaskedSeq):
            if unmaskedBase.upper() == hardmaskedBase.upper():
                softmaskedBase = unmaskedBase.upper()
            else:
                if not hardmaskedBase.upper() == 'N':
                    print("Warning: encountered differing base: %s %s" % (unmaskedBase, hardmaskedBase))
                softmaskedBase = unmaskedBase.lower()
            softmaskedSeq += softmaskedBase
        bioio.fastaWrite(softmasked, unmaskedName, softmaskedSeq)
Example #3
0
 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()