def testCigarReadWrite(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
cigarNumber = random.choice(xrange(10))
l = [ getRandomPairwiseAlignment() for i in xrange(cigarNumber) ]
fileHandle = open(tempFile, 'w')
for cigar in l:
cigarWrite(fileHandle, cigar)
fileHandle.close()
fileHandle = open(tempFile, 'r')
l.reverse()
for cigar in cigarRead(fileHandle):
cigarWrite(sys.stdout, l[-1])
cigarWrite(sys.stdout, cigar)
assert cigar == l.pop()
assert len(l) == 0
fileHandle.close()
def testCigarReadWrite(self):
"""Tests the C code for reading and writing cigars against the python parser for cigars.
"""
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
pairwiseAlignmentNumber = random.choice(xrange(10))
l = [
getRandomPairwiseAlignment()
for i in xrange(pairwiseAlignmentNumber)
]
fileHandle = open(tempFile, 'w')
keepProbs = random.random() > 0.5
if keepProbs == False:
for pA in l:
for op in pA.operationList:
op.score = 0.0
for pairwiseAlignment in l:
cigarWrite(fileHandle, pairwiseAlignment, keepProbs)
fileHandle.close()
#Now call sonLib_cigarsTest and read and write chains
command = "sonLib_cigarTest %s %s" % (tempFile, keepProbs)
#return
system(command)
#Now check the chain is okay
fileHandle = open(tempFile, 'r')
l.reverse()
for pairwiseAlignment in cigarRead(fileHandle):
pairwiseAlignment2 = l.pop()
cigarWrite(sys.stdout, pairwiseAlignment, keepProbs)
cigarWrite(sys.stdout, pairwiseAlignment2, keepProbs)
assert pairwiseAlignment == pairwiseAlignment2
assert len(l) == 0
fileHandle.close()
def testCigarReadWrite(self):
"""Tests the C code for reading and writing cigars against the python parser for cigars.
"""
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
pairwiseAlignmentNumber = random.choice(xrange(10))
l = [ getRandomPairwiseAlignment() for i in xrange(pairwiseAlignmentNumber) ]
fileHandle = open(tempFile, 'w')
keepProbs = random.random() > 0.5
if keepProbs == False:
for pA in l:
for op in pA.operationList:
op.score = 0.0
for pairwiseAlignment in l:
cigarWrite(fileHandle, pairwiseAlignment, keepProbs)
fileHandle.close()
#Now call sonLib_cigarsTest and read and write chains
command = "sonLib_cigarTest %s %s" % (tempFile, keepProbs)
#return
system(command)
#Now check the chain is okay
fileHandle = open(tempFile, 'r')
l.reverse()
for pairwiseAlignment in cigarRead(fileHandle):
pairwiseAlignment2 = l.pop()
cigarWrite(sys.stdout, pairwiseAlignment, keepProbs)
cigarWrite(sys.stdout, pairwiseAlignment2, keepProbs)
assert pairwiseAlignment == pairwiseAlignment2
assert len(l) == 0
fileHandle.close()