def _assertWrite(self, filePrefix, dataType, contents):
s = Setup(filePrefix, len(contents), dataType, 1, None)
of = OutputFile(s.path, s.filePrefix, len(contents))
for i in contents:
of.write(i)
of.close()
self.assertTrue(os.path.exists(s.fn))
fileContents = [i for i in memmap(s.fn, dataType, mode='r')]
self.assertListsOrDicts(contents, fileContents)
class OutputIndexFilePair(object):
def __init__(self, path, chrSize, startFile, endFile):
self._path = path
self._chrSize = chrSize
self._startFile = startFile
self._endFile = endFile
def writeIndexes(self):
numIndexElements = int(math.ceil(1.0 * self._chrSize / CompBinManager.getIndexBinSize()))
self._leftIndexFile = OutputFile(self._path, 'leftIndex', numIndexElements, allowAppend=False)
self._rightIndexFile = OutputFile(self._path, 'rightIndex', numIndexElements, allowAppend=False)
if self._startFile:
lefts = self._startFile.getContents()
else:
lefts = np.r_[0, self._endFile.getContents()[:-1]]
if self._endFile:
rights = self._endFile.getContents()
if not self._startFile:
rights = rights[1:]
else:
rights = self._startFile.getContents() + 1
bin_i = 0
i = 0
for i, right in enumerate(rights):
while right > (bin_i) * CompBinManager.getIndexBinSize():
self._leftIndexFile.write(i)
bin_i += 1
bin_j = 0
j = 0
for j, left in enumerate(lefts):
while left >= (bin_j+1) * CompBinManager.getIndexBinSize():
self._rightIndexFile.write(j)
bin_j += 1
self._fillRestOfIndexFile(bin_i, i+1, self._leftIndexFile)
self._fillRestOfIndexFile(bin_j, j+1, self._rightIndexFile)
def _fillRestOfIndexFile(self, numFilled, fillValue, indexFile):
for i in xrange( len(indexFile) - numFilled ):
indexFile.write(fillValue)
def close(self):
self._leftIndexFile.close()
self._rightIndexFile.close()
