def __init__(self, line, percent_slop=0, fixed_slop=0):
'''
Initialize with slop for probabilities
'''
self.l = line
(self.sv_type,
chr_l,
chr_r,
self.strands,
start_l,
end_l,
start_r,
end_r,
m) = l_bp.split_v(line)
try:
self.left = BreakpointInterval(chr_l, start_l, end_l, self.floats_from_tag(m, 'PRPOS'))
self.right = BreakpointInterval(chr_r, start_r, end_r, self.floats_from_tag(m, 'PREND'))
except RuntimeError as e:
raise MissingProbabilitiesException(str(e))
if ((percent_slop > 0) or (fixed_slop > 0)):
self.left.pad_slop(percent_slop, fixed_slop)
self.right.pad_slop(percent_slop, fixed_slop)
def __init__(self, line, percent_slop=0, fixed_slop=0):
'''
Initialize with slop for probabilities
'''
self.l = line
(self.sv_type,
chr_l,
chr_r,
self.strands,
start_l,
end_l,
start_r,
end_r,
m) = l_bp.split_v(line)
try:
self.left = BreakpointInterval(chr_l, start_l, end_l, self.floats_from_tag(m, 'PRPOS'))
self.right = BreakpointInterval(chr_r, start_r, end_r, self.floats_from_tag(m, 'PREND'))
except RuntimeError as e:
raise MissingProbabilitiesException(str(e))
if ((percent_slop > 0) or (fixed_slop > 0)):
self.left.pad_slop(percent_slop, fixed_slop)
self.right.pad_slop(percent_slop, fixed_slop)
def print_var_line(l):
A = l.rstrip().split('\t')
if A[4] not in ['<DEL>', '<DUP>', '<INV>']:
[sv_type, chr_l, chr_r, start_l, end_l, start_r, end_r,
m] = l_bp.split_v(l)
CHROM = chr_r
POS = m['END']
ID = A[2] + '_2'
REF = 'N'
ALT = ''
if ']' in A[4]:
ALT = '[' + chr_l + ':' + A[1] + '[N'
else:
ALT = 'N]' + chr_l + ':' + A[1] + ']'
QUAL = A[5]
FILTER = '.'
SVTYPE = 'BND'
STRANDS = m['STRANDS']
SVLEN = '0'
CIPOS = m['CIEND']
CIEND = m['CIPOS']
CIPOS95 = m['CIEND95']
CIEND95 = m['CIPOS95']
IMPRECISE = 'IMPRECISE'
SU = m['SU']
PE = m['PE']
SR = m['SR']
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
EVENT = m['EVENT']
SECONDARY = 'SECONDARY'
MATEID = A[2] + '_1'
INFO = ';'.join([
'SVTYPE=' + str(SVTYPE), 'STRANDS=' + str(STRANDS),
'SVLEN=' + str(SVLEN), 'CIPOS=' + str(CIPOS),
'CIEND=' + str(CIEND), 'CIPOS95=' + str(CIPOS95),
'CIEND95=' + str(CIEND95),
str(IMPRECISE),
str(SECONDARY), 'SU=' + str(SU), 'PE=' + str(PE), 'SR=' + str(SR),
'PRPOS=' + str(PRPOS), 'PREND=' + str(PREND),
'SNAME=' + str(SNAME), 'EVENT=' + str(EVENT),
'MATEID=' + str(MATEID)
])
O = [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
A[7] += ';MATEID=' + A[2] + '_2'
A[2] += '_1'
print '\t'.join(A[:8])
print '\t'.join([str(o) for o in O])
else:
print l
def __init__(self, line, percent_slop=0, fixed_slop=0):
'''
Initialize with slop for probabilities
'''
self.l = line
(self.sv_type,
self.chr_l,
self.chr_r,
self.strands,
self.start_l,
self.end_l,
self.start_r,
self.end_r,
m) = l_bp.split_v(line)
# TODO Handle missing PRPOS and PREND with intelligent message. Pull out into method.
self.p_l = [float(x) for x in m['PRPOS'].split(',')]
self.p_r = [float(x) for x in m['PREND'].split(',')]
slop_prob = 1e-100 # FIXME This is a constant. Pull out to make more obvious
if ((percent_slop > 0) or (fixed_slop > 0)):
l_slop = int(max(percent_slop * (self.end_l - self.start_l + 1), fixed_slop))
r_slop = int(max(percent_slop * (self.end_r - self.start_r + 1), fixed_slop))
# pad each interval with slop_prob on each side. TODO This should be a method
self.start_l = self.start_l - l_slop
self.end_l = self.end_l + l_slop
new_p_l = [slop_prob] * l_slop + self.p_l + [slop_prob] * l_slop
self.start_r = self.start_r - r_slop
self.end_r = self.end_r + r_slop
new_p_r = [slop_prob] * r_slop + self.p_r + [slop_prob] * r_slop
# chew off overhang if self.start_l or self.start_r less than 0 TODO This should also be a method
if self.start_l < 0:
new_p_l = new_p_l[-self.start_l:]
self.start_l = 0
if self.start_r < 0:
new_p_r = new_p_r[-self.start_r:]
self.start_r = 0
# normalize so each probability curve sums to 1. TODO Should be a method
sum_p_l = sum(new_p_l)
self.p_l = [float(x)/sum_p_l for x in new_p_l]
sum_p_r = sum(new_p_r)
self.p_r = [float(x)/sum_p_r for x in new_p_r]
def __init__(self, line, percent_slop=0, fixed_slop=0):
'''
Initialize with slop for probabilities
'''
self.l = line
(self.sv_type, self.chr_l, self.chr_r, self.strands, self.start_l,
self.end_l, self.start_r, self.end_r, m) = l_bp.split_v(line)
# TODO Handle missing PRPOS and PREND with intelligent message. Pull out into method.
self.p_l = [float(x) for x in m['PRPOS'].split(',')]
self.p_r = [float(x) for x in m['PREND'].split(',')]
slop_prob = 1e-100 # FIXME This is a constant. Pull out to make more obvious
if ((percent_slop > 0) or (fixed_slop > 0)):
l_slop = int(
max(percent_slop * (self.end_l - self.start_l + 1),
fixed_slop))
r_slop = int(
max(percent_slop * (self.end_r - self.start_r + 1),
fixed_slop))
# pad each interval with slop_prob on each side. TODO This should be a method
self.start_l = self.start_l - l_slop
self.end_l = self.end_l + l_slop
new_p_l = [slop_prob] * l_slop + self.p_l + [slop_prob] * l_slop
self.start_r = self.start_r - r_slop
self.end_r = self.end_r + r_slop
new_p_r = [slop_prob] * r_slop + self.p_r + [slop_prob] * r_slop
# chew off overhang if self.start_l or self.start_r less than 0 TODO This should also be a method
if self.start_l < 0:
new_p_l = new_p_l[-self.start_l:]
self.start_l = 0
if self.start_r < 0:
new_p_r = new_p_r[-self.start_r:]
self.start_r = 0
# normalize so each probability curve sums to 1. TODO Should be a method
sum_p_l = sum(new_p_l)
self.p_l = [float(x) / sum_p_l for x in new_p_l]
sum_p_r = sum(new_p_r)
self.p_r = [float(x) / sum_p_r for x in new_p_r]
def print_var_line(l):
A = l.rstrip().split('\t')
if A[4] == '<INV>' and ('--:0' in A[7] or '++:0' in A[7]):
[sv_type,chr_l,chr_r,strands,start_l,end_l,start_r,end_r,m] = \
l_bp.split_v(l)
STRAND_DICT = dict(x.split(':') for x in m['STRANDS'].split(','))
for o in STRAND_DICT.keys():
if STRAND_DICT[o] == '0':
del(STRAND_DICT[o])
STRANDS = ','.join(['%s:%s' % (o,STRAND_DICT[o]) for o in STRAND_DICT])
if STRANDS[:2] == '++':
ALT = 'N]' + chr_l + ':' + m['END'] + ']'
elif STRANDS[:2] == '--':
ALT = '[' + chr_l + ':' + m['END'] + '[N'
SVTYPE = 'BND'
CIPOS = m['CIEND']
CIEND = m['CIPOS']
CIPOS95 = m['CIEND95']
CIEND95 = m['CIPOS95']
IMPRECISE = 'IMPRECISE'
SU = m['SU']
PE = m['PE']
SR = m['SR']
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
EVENT = A[2]
A[4] = ALT
A[7] = ';'.join(['SVTYPE=' + str(SVTYPE),
'STRANDS=' + str(STRANDS),
'CIPOS=' + str(CIPOS),
'CIEND=' + str(CIEND),
'CIPOS95=' + str(CIPOS95),
'CIEND95=' + str(CIEND95),
str(IMPRECISE),
'SU=' + str(SU),
'PE=' + str(PE),
'SR=' + str(SR),
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'SNAME=' + str(SNAME),
'EVENT=' + str(EVENT)])
# reconstruct the line
l = '\t'.join(A)
if A[4] not in ['<DEL>', '<DUP>', '<INV>']:
[sv_type,chr_l,chr_r,strands,start_l,end_l,start_r,end_r,m] = \
l_bp.split_v(l)
CHROM = chr_r
POS = m['END']
ID = A[2] + '_2'
REF = 'N'
ALT = ''
if A[4][0] == '[':
ALT = '[' + chr_l + ':' + A[1] + '[N'
elif A[4][0] == ']':
ALT = 'N[' + chr_l + ':' + A[1] + '['
elif A[4][-1] == '[':
ALT = ']' + chr_l + ':' + A[1] + ']N'
elif A[4][-1] == ']':
ALT = 'N]' + chr_l + ':' + A[1] + ']'
QUAL = A[5]
FILTER = '.'
SVTYPE = 'BND'
STRANDS = m['STRANDS']
CIPOS = m['CIEND']
CIEND = m['CIPOS']
CIPOS95 = m['CIEND95']
CIEND95 = m['CIPOS95']
IMPRECISE = 'IMPRECISE'
SU = m['SU']
PE = m['PE']
SR = m['SR']
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
EVENT = A[2]
SECONDARY = 'SECONDARY'
MATEID=A[2] + '_1'
INFO = ';'.join(['SVTYPE=' + str(SVTYPE),
'STRANDS=' + str(STRANDS),
'CIPOS=' + str(CIPOS),
'CIEND=' + str(CIEND),
'CIPOS95=' + str(CIPOS95),
'CIEND95=' + str(CIEND95),
str(IMPRECISE),
str(SECONDARY),
'SU=' + str(SU),
'PE=' + str(PE),
'SR=' + str(SR),
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'SNAME=' + str(SNAME),
'EVENT=' + str(EVENT),
'MATEID=' + str(MATEID)])
O = [CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO]
A[7] += ';MATEID=' + A[2] + '_2'
A[2] += '_1'
print '\t'.join(A[:8])
print '\t'.join([str(o) for o in O])
else:
print '\t'.join(A[:8])
def print_var_line(l):
A = l.rstrip().split('\t')
if A[4] not in ['<DEL>', '<DUP>', '<INV>']:
[sv_type,chr_l,chr_r,start_l,end_l,start_r,end_r,m] = l_bp.split_v(l)
CHROM = chr_r
POS = m['END']
ID = A[2] + '_2'
REF = 'N'
ALT = ''
if ']' in A[4]:
ALT = '[' + chr_l + ':' + A[1] + '[N'
else:
ALT = 'N]' + chr_l + ':' + A[1] + ']'
QUAL = A[5]
FILTER = '.'
SVTYPE = 'BND'
STRANDS = m['STRANDS']
SVLEN = '0'
CIPOS = m['CIEND']
CIEND = m['CIPOS']
CIPOS95 = m['CIEND95']
CIEND95 = m['CIPOS95']
IMPRECISE = 'IMPRECISE'
SU = m['SU']
PE = m['PE']
SR = m['SR']
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
EVENT = m['EVENT']
SECONDARY = 'SECONDARY'
MATEID=A[2] + '_1'
INFO = ';'.join(['SVTYPE=' + str(SVTYPE),
'STRANDS=' + str(STRANDS),
'SVLEN=' + str(SVLEN),
'CIPOS=' + str(CIPOS),
'CIEND=' + str(CIEND),
'CIPOS95=' + str(CIPOS95),
'CIEND95=' + str(CIEND95),
str(IMPRECISE),
str(SECONDARY),
'SU=' + str(SU),
'PE=' + str(PE),
'SR=' + str(SR),
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'SNAME=' + str(SNAME),
'EVENT=' + str(EVENT),
'MATEID=' + str(MATEID)])
O = [CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO]
A[7] += ';MATEID=' + A[2] + '_2'
A[2] += '_1'
print '\t'.join(A[:8])
print '\t'.join([str(o) for o in O])
else:
print l
def print_var_line(l):
A = l.rstrip().split("\t")
if A[4] == "<INV>" and ("--:0" in A[7] or "++:0" in A[7]):
[sv_type, chr_l, chr_r, strands, start_l, end_l, start_r, end_r, m] = l_bp.split_v(l)
STRAND_DICT = dict(x.split(":") for x in m["STRANDS"].split(","))
for o in STRAND_DICT.keys():
if STRAND_DICT[o] == "0":
del (STRAND_DICT[o])
STRANDS = ",".join(["%s:%s" % (o, STRAND_DICT[o]) for o in STRAND_DICT])
if STRANDS[:2] == "++":
ALT = "N]" + chr_l + ":" + m["END"] + "]"
elif STRANDS[:2] == "--":
ALT = "[" + chr_l + ":" + m["END"] + "[N"
SVTYPE = "BND"
CIPOS = m["CIEND"]
CIEND = m["CIPOS"]
CIPOS95 = m["CIEND95"]
CIEND95 = m["CIPOS95"]
IMPRECISE = "IMPRECISE"
SU = m["SU"]
PE = m["PE"]
SR = m["SR"]
PRPOS = m["PREND"]
PREND = m["PRPOS"]
SNAME = m["SNAME"]
EVENT = A[2]
A[4] = ALT
A[7] = ";".join(
[
"SVTYPE=" + str(SVTYPE),
"STRANDS=" + str(STRANDS),
"CIPOS=" + str(CIPOS),
"CIEND=" + str(CIEND),
"CIPOS95=" + str(CIPOS95),
"CIEND95=" + str(CIEND95),
str(IMPRECISE),
"SU=" + str(SU),
"PE=" + str(PE),
"SR=" + str(SR),
"PRPOS=" + str(PRPOS),
"PREND=" + str(PREND),
"SNAME=" + str(SNAME),
"EVENT=" + str(EVENT),
]
)
# reconstruct the line
l = "\t".join(A)
if A[4] not in ["<DEL>", "<DUP>", "<INV>"]:
[sv_type, chr_l, chr_r, strands, start_l, end_l, start_r, end_r, m] = l_bp.split_v(l)
CHROM = chr_r
POS = m["END"]
ID = A[2] + "_2"
REF = "N"
ALT = ""
if A[4][0] == "[":
ALT = "[" + chr_l + ":" + A[1] + "[N"
elif A[4][0] == "]":
ALT = "N[" + chr_l + ":" + A[1] + "["
elif A[4][-1] == "[":
ALT = "]" + chr_l + ":" + A[1] + "]N"
elif A[4][-1] == "]":
ALT = "N]" + chr_l + ":" + A[1] + "]"
QUAL = A[5]
FILTER = "."
SVTYPE = "BND"
STRANDS = m["STRANDS"]
CIPOS = m["CIEND"]
CIEND = m["CIPOS"]
CIPOS95 = m["CIEND95"]
CIEND95 = m["CIPOS95"]
IMPRECISE = "IMPRECISE"
SU = m["SU"]
PE = m["PE"]
SR = m["SR"]
PRPOS = m["PREND"]
PREND = m["PRPOS"]
SNAME = m["SNAME"]
EVENT = A[2]
SECONDARY = "SECONDARY"
MATEID = A[2] + "_1"
INFO = ";".join(
[
"SVTYPE=" + str(SVTYPE),
"STRANDS=" + str(STRANDS),
"CIPOS=" + str(CIPOS),
"CIEND=" + str(CIEND),
"CIPOS95=" + str(CIPOS95),
"CIEND95=" + str(CIEND95),
str(IMPRECISE),
str(SECONDARY),
"SU=" + str(SU),
"PE=" + str(PE),
"SR=" + str(SR),
"PRPOS=" + str(PRPOS),
"PREND=" + str(PREND),
"SNAME=" + str(SNAME),
"EVENT=" + str(EVENT),
"MATEID=" + str(MATEID),
]
)
O = [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
A[7] += ";MATEID=" + A[2] + "_2"
A[2] += "_1"
print "\t".join(A[:8])
print "\t".join([str(o) for o in O])
else:
print "\t".join(A[:8])
