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 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)
def testPWMParser(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
pWM = getRandomPWM()
fileHandle = open(tempFile, 'w')
pWMWrite(fileHandle, pWM)
fileHandle.close()
fileHandle = open(tempFile, 'r')
pWM2 = pWMRead(fileHandle)
fileHandle.close()
for i in xrange(0, len(pWM)):
pWM[i] == pWM2[i]
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()
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()
