def mhsmidkernelsmooth(bamfile, bwfile, maxinsert=80, mininsert=1, paired=False, kernelsize=30):
bamfor = Baminfo.Baminfo(bamfile)
bw = pyBigWig.open(bwfile, "w")
bw.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
mhsmidcount = mhsbam.mhsmidcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, maxinsert=maxinsert, mininsert=mininsert, paired=paired)
mhsmidsmoothed = kernelsmooth(mhsmidcount, 1, end, end, kernelsize)
if mhsmidsmoothed:
starts = list()
values = list()
for start in sorted(mhsmidsmoothed):
starts.append(start)
values.append(float(mhsmidsmoothed[start]))
bw.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bw.close()
def mhsmidkernelsmooth(bamfile, bwfile, maxinsert=80, mininsert=1, paired=False, kernelsize=30):
bamfor = Baminfo.Baminfo(bamfile)
bw = pyBigWig.open(bwfile, "w")
bw.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
mhsmidcount = mhsbam.mhsmidcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, maxinsert=maxinsert, mininsert=mininsert, paired=paired)
mhsmidsmoothed = kernelsmooth(mhsmidcount, 1, end, end, kernelsize)
if mhsmidsmoothed:
starts = list()
values = list()
for start in sorted(mhsmidsmoothed):
starts.append(start)
values.append(float(mhsmidsmoothed[start]))
bw.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bw.close()
def test_openmhs_pairedshort(self):
res = mhsbam.mhsmidcount(self.pairedbamnps,
chromosome='Chr1',
start=1,
end=300,
paired=True)
self.assertEqual(res[115], 2)
def test_openmhs_pairedlong_empty(self):
res = mhsbam.mhsmidcount(self.pairedbamnps,
chromosome='Chr2',
start=1,
end=300,
maxinsert=180,
paired=True)
self.assertFalse(res)
def test_openmhs_pairedlong(self):
res = mhsbam.mhsmidcount(self.pairedbamnps,
chromosome='Chr1',
start=1,
end=300,
maxinsert=180,
paired=True)
self.assertEqual(res[251], 3)
def midextendtobw(bamfile, bwfile, maxinsert, mininsert, paired=False, extend=80):
bamfor = Baminfo.Baminfo(bamfile)
bw = pyBigWig.open(bwfile, "w")
bw.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
mhsmidcount = mhsbam.mhsmidcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, maxinsert=maxinsert, mininsert=mininsert, paired=paired)
if mhsmidcount:
extended = dict()
for midnow in mhsmidcount:
halfextend = int(extend/2)
rangestart = 0-halfextend
rangeend = halfextend+1
for i in range(rangestart, rangeend):
nowsite = i + midnow
if nowsite < 1:
continue
if nowsite > end:
continue
if nowsite in extended:
extended[nowsite] += mhsmidcount[midnow]
else:
extended[nowsite] = mhsmidcount[midnow]
starts = list()
values = list()
for nowsite in sorted(extended):
starts.append(nowsite)
values.append(float(extended[nowsite]))
bw.addEntries(chromosome, starts=starts, values=values, span=1, step=1)
bw.close()
def test_openmhs_pairedlong_empty(self):
res = mhsbam.mhsmidcount(self.pairedbamnps, chromosome='Chr2', start=1, end=300, maxinsert=180, paired=True)
self.assertFalse(res)
def test_openmhs_pairedlong(self):
res = mhsbam.mhsmidcount(self.pairedbamnps, chromosome='Chr1', start=1, end=300, maxinsert=180, paired=True)
self.assertEqual(res[251], 3)
def test_openmhs_pairedshort(self):
res = mhsbam.mhsmidcount(self.pairedbamnps, chromosome='Chr1', start=1, end=300, paired=True)
self.assertEqual(res[115], 2)
