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 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 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)