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 createDirPath(trackName, genome, chr=None, allowOverlaps=False, basePath=Config.PROCESSED_DATA_PATH):
"""
>>> createDirPath(['trackname'],'genome','chr1')
'/100000/noOverlaps/genome/trackname/chr1'
"""
from gtrackcore_memmap.util.CompBinManager import CompBinManager
if len(trackName)>0 and trackName[0] == 'redirect':
genome = trackName[1]
chr = trackName[2]
#trackName[3] is description
trackName = trackName[4:]
#print [basePath, str(CompBinManager.getIndexBinSize()), ('withOverlaps' if allowOverlaps else 'noOverlaps'), genome] +\
# list(trackName) + ([chr] if chr is not None else [])
return os.sep.join( [basePath, str(CompBinManager.getIndexBinSize()), ('withOverlaps' if allowOverlaps else 'noOverlaps'), genome] +\
list(trackName) + ([chr] if chr is not None else []) )
