def dhsstrandtobw(bamfile, rbwfile, fbwfile, library='Duke', nagtiverev=True):
"""
:param bamfile:
:param bwfile:
:param library:Duke or Washington
Duke: |=====>
<=====|
Washington: |===========|
Out put cutting site '|'
:param nagtiverev: - Strand use nagative score
:return:
"""
bamfor = Baminfo.Baminfo(bamfile)
bwf = pyBigWig.open(fbwfile, "w")
bwr = pyBigWig.open(rbwfile, "w")
bwf.addHeader(list(bamfor.chrlen.items()))
bwr.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
dhscut = dhsbam.dhstrandcutcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, library=library)
if dhscut['+']:
starts = list()
values = list()
for start in sorted(dhscut['+']):
starts.append(start)
values.append(float(dhscut['+'][start]))
bwf.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
if dhscut['-']:
starts = list()
values = list()
for start in sorted(dhscut['-']):
starts.append(start)
if nagtiverev:
values.append(0 - float(dhscut['-'][start]))
else:
values.append(float(dhscut['-'][start]))
bwr.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bwf.close()
bwr.close()
def dhsstrandtobw(bamfile, rbwfile, fbwfile, library='Duke', nagtiverev=True):
"""
:param bamfile:
:param bwfile:
:param library:Duke or Washington
Duke: |=====>
<=====|
Washington: |===========|
Out put cutting site '|'
:param nagtiverev: - Strand use nagative score
:return:
"""
bamfor = Baminfo.Baminfo(bamfile)
bwf = pyBigWig.open(fbwfile, "w")
bwr = pyBigWig.open(rbwfile, "w")
bwf.addHeader(list(bamfor.chrlen.items()))
bwr.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
dhscut = dhsbam.dhstrandcutcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, library=library)
if dhscut['+']:
starts = list()
values = list()
for start in sorted(dhscut['+']):
starts.append(start)
values.append(float(dhscut['+'][start]))
bwf.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
if dhscut['-']:
starts = list()
values = list()
for start in sorted(dhscut['-']):
starts.append(start)
if nagtiverev:
values.append(0 - float(dhscut['-'][start]))
else:
values.append(float(dhscut['-'][start]))
bwr.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bwf.close()
bwr.close()
def dhextendtobw(bamfile, bwfile, extendsize=20, library='Duke'):
"""
:param bamfile:
:param bwfile:
:param library:Duke or Washington
Duke: |=====>
<=====|
Washington: |===========|
Out put cutting site '|'
:param nagtiverev: - Strand use nagative score
:return:
"""
bamfor = Baminfo.Baminfo(bamfile)
bw = pyBigWig.open(bwfile, "w")
bw.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
dhscut = dhsbam.dhstrandcutcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, library=library)
dhsext = dict()
if dhscut['+']:
# starts = list()
#
# values = list()
for start in sorted(dhscut['+']):
# starts.append(start)
#
# values.append(float(dhscut['+'][start]))
for i in range(0, extendsize):
nowsite = start + i
if 0 < nowsite < end:
if nowsite in dhsext:
dhsext[nowsite] += float(dhscut['+'][start])
else:
dhsext[nowsite] = float(dhscut['+'][start])
if dhscut['-']:
starts = list()
values = list()
for start in sorted(dhscut['-']):
for i in range(0 - extendsize, 0):
nowsite = start + i
if 0 < nowsite < end:
if nowsite in dhsext:
dhsext[nowsite] += float(dhscut['-'][start])
else:
dhsext[nowsite] = float(dhscut['-'][start])
starts = list()
values = list()
for nowsite in sorted(dhsext):
starts.append(nowsite)
values.append(dhsext[nowsite])
bw.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bw.close()
def dhextendtobw(bamfile, bwfile, extendsize=20, library='Duke'):
"""
:param bamfile:
:param bwfile:
:param library:Duke or Washington
Duke: |=====>
<=====|
Washington: |===========|
Out put cutting site '|'
:param nagtiverev: - Strand use nagative score
:return:
"""
bamfor = Baminfo.Baminfo(bamfile)
bw = pyBigWig.open(bwfile, "w")
bw.addHeader(list(bamfor.chrlen.items()))
for chromosome in bamfor.chrlen:
end = bamfor.chrlen[chromosome]
dhscut = dhsbam.dhstrandcutcount(bamfile=bamfile, chromosome=chromosome, start=1,
end=end, library=library)
dhsext = dict()
if dhscut['+']:
# starts = list()
#
# values = list()
for start in sorted(dhscut['+']):
# starts.append(start)
#
# values.append(float(dhscut['+'][start]))
for i in range(0, extendsize):
nowsite = start + i
if 0 < nowsite < end:
if nowsite in dhsext:
dhsext[nowsite] += float(dhscut['+'][start])
else:
dhsext[nowsite] = float(dhscut['+'][start])
if dhscut['-']:
starts = list()
values = list()
for start in sorted(dhscut['-']):
for i in range(0 - extendsize, 0):
nowsite = start + i
if 0 < nowsite < end:
if nowsite in dhsext:
dhsext[nowsite] += float(dhscut['-'][start])
else:
dhsext[nowsite] = float(dhscut['-'][start])
starts = list()
values = list()
for nowsite in sorted(dhsext):
starts.append(nowsite)
values.append(dhsext[nowsite])
bw.addEntries(chromosome, starts=starts, values=values,
span=1, step=1)
bw.close()