def __init__(self, fromH1, a, b): #a=0.5, b=25):
self._fromH1 = fromH1
self._a = a
self._b = b
if self._fromH1:
self._underlyingPval = r.rbeta(1, self._a, self._b) #[0]
else:
self._underlyingPval = r.runif(1) #[0]
def __iter__(self):
from proto.RSetup import r
pos = 0
maxPos = self._getChrLen()
while True:
#dist between segs
if r.runif(1) < self.interProb:
pos += int(max(1, r.rexp(1, self.interRate)))
else:
pos += int(max(1, r.rexp(1, self.intraRate)))
start = pos
#segLen
pos += int(r.runif(1, self.minSegLen, self.maxSegLen))
end = pos
if pos < maxPos:
yield [start, end]
else:
break
def __iter__(self):
from proto.RSetup import r
pos = 0
maxPos = self._getChrLen()
while True:
if r.runif(1) < self.interProb:
pos += int(max(1, r.rexp(1, self.interRate)))
else:
pos += int(max(1, r.rexp(1, self.intraRate)))
if pos < maxPos:
yield [pos, pos + 1]
else:
break
def __iter__(self):
from proto.RSetup import r
chr = self.chr
trackName1, genome = self.trackName1, self.genome
factor = self.factor
region = GenomeRegion(genome, chr, 0,
GenomeInfo.getChrLen(genome, chr))
track1 = PlainTrack(trackName1)
tv1 = track1.getTrackView(region)
vals1 = tv1.valsAsNumpyArray()
#scale between 0 and 1..:
minVal, maxVal = vals1.min(), vals1.max()
vals1 = (vals1 - minVal) * (1 / (maxVal - minVal))
for pos in xrange(len(vals1)):
#print r.runif(1), vals1[pos]
if r.runif(1) < factor * vals1[pos]:
yield [pos, pos + 1]
def __iter__(self):
from proto.RSetup import r
#maxPos = self._getChrLen()
maxPos = self.chrMax
minPos = self.chrMin
pos = minPos
while True:
runif = r.runif(1)
if runif < self.interProb:
rexp = r.rexp(1, self.interRate)
pos += int(max(1, rexp)) # among clusters
else:
rexp = r.rexp(1, self.intraRate) # inside cluster
pos += int(max(1, rexp))
if pos < maxPos:
yield [pos, pos + 1]
else:
break