def readValuesPyBigWig(self, reference, start, end):
"""
Use pyBigWig package to read a BigWig file for the
given range and return a protocol object.
pyBigWig returns an array of values that fill the query range.
Not sure if it is possible to get the step and span.
This method trims NaN values from the start and end.
pyBigWig throws an exception if end is outside of the
reference range. This function checks the query range
and throws its own exceptions to avoid the ones thrown
by pyBigWig.
"""
if not self.checkReference(reference):
raise exceptions.ReferenceNameNotFoundException(reference)
if start < 0:
start = 0
bw = pyBigWig.open(self._sourceFile)
referenceLen = bw.chroms(reference)
if referenceLen is None:
raise exceptions.ReferenceNameNotFoundException(reference)
if end > referenceLen:
end = referenceLen
if start >= end:
raise exceptions.ReferenceRangeErrorException(
reference, start, end)
data = protocol.Continuous()
curStart = start
curEnd = curStart + self._INCREMENT
while curStart < end:
if curEnd > end:
curEnd = end
for i, val in enumerate(bw.values(reference, curStart, curEnd)):
if not math.isnan(val):
if len(data.values) == 0:
data.start = curStart + i
data.values.append(val)
if len(data.values) == self._MAX_VALUES:
yield data
data = protocol.Continuous()
elif len(data.values) > 0:
# data.values.append(float('NaN'))
yield data
data = protocol.Continuous()
curStart = curEnd
curEnd = curStart + self._INCREMENT
bw.close()
if len(data.values) > 0:
yield data
def __init__(self, reference, start, end):
self._queryReference = reference
self._queryStart = start
self._queryEnd = end
self._mode = None
self._span = 1
self._step = 1
self._data = protocol.Continuous()
self._position = None
def _generateSimulatedContinuous(self, randomNumberGenerator):
continuous = protocol.Continuous()
continuous.start = randomNumberGenerator.randint(1000, 2000)
continuous.values = [100, 200.3, 400]