def combine_pdfs(BP, c, use_product, weighting_scheme):
L = []
R = []
for b_i in c:
b = BP[b_i]
L.append([b.left.start, b.left.end, b.left.p])
R.append([b.right.start, b.right.end, b.right.p])
[start_R, end_R, a_R] = l_bp.align_intervals(R)
[start_L, end_L, a_L] = l_bp.align_intervals(L)
p_L = [0] * len(a_L[0])
p_R = [0] * len(a_R[0])
wts = [1] * len(c)
for c_i in range(len(c)):
if weighting_scheme == 'evidence_wt':
A = BP[c[c_i]].l.rstrip().split('\t', 10)
m = l_bp.to_map(A[7])
wt = int(m['SU'])
#sys.stderr.write("wt\t0\t"+str(wt)+"\n")
a_L[c_i] = [wt * ali for ali in a_L[c_i]]
a_R[c_i] = [wt * ari for ari in a_R[c_i]]
elif weighting_scheme == 'carrier_wt':
A = BP[c[c_i]].l.rstrip().split('\t', 10)
m = l_bp.to_map(A[7])
wt = 1
if 'SNAME' in m:
wt = len(m['SNAME'].split(','))
a_L[c_i] = [wt * ali for ali in a_L[c_i]]
a_R[c_i] = [wt * ari for ari in a_R[c_i]]
for i in range(len(a_L[c_i])):
#sys.stderr.write("L\t"+str(i)+"\t"+str(c_i)+"\t"+str(a_L[c_i][i])+"\n")
p_L[i] += a_L[c_i][i]
for i in range(len(a_R[c_i])):
#sys.stderr.write("R\t"+str(i)+"\t"+str(c_i)+"\t"+str(a_R[c_i][i])+"\n")
p_R[i] += a_R[c_i][i]
ALG = 'SUM'
if use_product:
pmax_i_L = p_L.index(max(p_L))
pmax_i_R = p_R.index(max(p_R))
miss = 0
for c_i in range(len(c)):
if (a_L[c_i][pmax_i_L] == 0) or (a_R[c_i][pmax_i_R] == 0):
miss += 1
if miss == 0:
ALG = "PROD"
ls_p_L = [ls.get_ls(1)] * len(a_L[0])
ls_p_R = [ls.get_ls(1)] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
ls_p_L[i] = ls.ls_multiply(ls_p_L[i],
ls.get_ls(a_L[c_i][i]))
for i in range(len(a_R[c_i])):
ls_p_R[i] = ls.ls_multiply(ls_p_R[i],
ls.get_ls(a_R[c_i][i]))
ls_sum_L = ls.get_ls(0)
ls_sum_R = ls.get_ls(0)
for ls_p in ls_p_L:
ls_sum_L = ls.ls_add(ls_sum_L, ls_p)
for ls_p in ls_p_R:
ls_sum_R = ls.ls_add(ls_sum_R, ls_p)
p_L = []
for ls_p in ls_p_L:
p_L.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_L)))
p_R = []
for ls_p in ls_p_R:
p_R.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_R)))
sum_L = sum(p_L)
sum_R = sum(p_R)
p_L = [x / sum_L for x in p_L]
p_R = [x / sum_L for x in p_R]
[clip_start_L, clip_end_L] = l_bp.trim(p_L)
[clip_start_R, clip_end_R] = l_bp.trim(p_R)
[new_start_L, new_end_L] = [start_L + clip_start_L, end_L - clip_end_L]
[new_start_R, new_end_R] = [start_R + clip_start_R, end_R - clip_end_R]
p_L = p_L[clip_start_L:len(p_L) - clip_end_L]
p_R = p_R[clip_start_R:len(p_R) - clip_end_R]
s_p_L = sum(p_L)
s_p_R = sum(p_R)
p_L = [x / s_p_L for x in p_L]
p_R = [x / s_p_R for x in p_R]
#sys.exit(1)
return new_start_L, new_start_R, p_L, p_R, ALG
def merge(BP, sample_order, v_id, use_product):
if len(BP) == 1:
A = BP[0].l.rstrip().split('\t')
#tack on id to SNAME
s_start = A[7].find('SNAME=')
s_end = A[7].find(';', s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + \
A[7][s_start:s_end] + \
':' + A[2] + \
A[7][s_end:]
else:
A[7] += ':' + A[2]
# reset the id to be unique in this file
v_id += 1
A[2] = str(v_id)
#clip out old mate id
s_start = A[7].find('MATEID=')
s_end = A[7].find(';', s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end + 1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#clip out old event id
s_start = A[7].find('EVENT=')
s_end = A[7].find(';', s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end + 1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#add new mate
A[7] += ';EVENT=' + A[2]
#add new alg
if use_product:
A[7] += ';ALG=PROD'
else:
A[7] += ';ALG=SUM'
print_var_line('\t'.join(A))
return v_id
#Sweep the set. Find the largest intersecting set. Remove it. Continue.
import heapq
BP.sort(key=lambda x: x.start_l)
BP_i = range(len(BP)) # index set of each node in the graph
C = []
while len(BP_i) > 0:
h_l = [
] #heap of left breakpoint end coordinates and node id (index). heapq is a min heap and the end coord is what will be used for the sorting.
max_c = []
max_c_len = 0
for i in BP_i:
# remove anything in the heap that doesn't intersect with the current breakpoint
while (len(h_l) > 0) and (h_l[0][0] < BP[i].start_l):
heapq.heappop(h_l)
heapq.heappush(h_l, (BP[i].end_l, i)) # add to the heap
# at this point everything in h_l intersects on the left
# but we need to take into account what is going on on the right
h_r = [] # heap with rightmost starts
h_l_i = [x[1] for x in h_l
] # this is all of the node ids on the heap currently
h_l_i.sort(
key=lambda x: BP[x].start_r) # sort them by their right start
for j in h_l_i:
# remove anything in the heap that doesn't intersect with the current breakpoint on the right end
while (len(h_r) > 0) and (h_r[0][0] < BP[j].start_r):
heapq.heappop(h_r)
# add something to the right heap
heapq.heappush(h_r, (BP[j].end_r, j))
if max_c_len < len(h_r):
# max clique! Register what nodes we have
max_c_len = len(h_r)
max_c = [y[1] for y in h_r]
C.append(max_c)
for c in max_c:
BP_i.remove(c)
for c in C:
L = []
R = []
for b_i in c:
b = BP[b_i]
L.append([b.start_l, b.end_l, b.p_l])
R.append([b.start_r, b.end_r, b.p_r])
[start_R, end_R, a_R] = l_bp.align_intervals(R)
[start_L, end_L, a_L] = l_bp.align_intervals(L)
p_L = [0] * len(a_L[0])
p_R = [0] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
p_L[i] += a_L[c_i][i]
for i in range(len(a_R[c_i])):
p_R[i] += a_R[c_i][i]
ALG = 'SUM'
if use_product:
pmax_i_L = p_L.index(max(p_L))
pmax_i_R = p_R.index(max(p_R))
miss = 0
for c_i in range(len(c)):
if (a_L[c_i][pmax_i_L] == 0) or (a_R[c_i][pmax_i_R] == 0):
miss += 1
if miss == 0:
ALG = "PROD"
ls_p_L = [ls.get_ls(1)] * len(a_L[0])
ls_p_R = [ls.get_ls(1)] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
ls_p_L[i] = ls.ls_multiply(ls_p_L[i],
ls.get_ls(a_L[c_i][i]))
for i in range(len(a_R[c_i])):
ls_p_R[i] = ls.ls_multiply(ls_p_R[i],
ls.get_ls(a_R[c_i][i]))
ls_sum_L = ls.get_ls(0)
ls_sum_R = ls.get_ls(0)
for ls_p in ls_p_L:
ls_sum_L = ls.ls_add(ls_sum_L, ls_p)
for ls_p in ls_p_R:
ls_sum_R = ls.ls_add(ls_sum_R, ls_p)
p_L = []
for ls_p in ls_p_L:
p_L.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_L)))
p_R = []
for ls_p in ls_p_R:
p_R.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_R)))
sum_L = sum(p_L)
sum_R = sum(p_R)
p_L = [x / sum_L for x in p_L]
p_R = [x / sum_L for x in p_R]
[clip_start_L, clip_end_L] = l_bp.trim(p_L)
[clip_start_R, clip_end_R] = l_bp.trim(p_R)
new_start_L = start_L + clip_start_L
new_end_L = end_L - clip_end_L
new_start_R = start_R + clip_start_R
new_end_R = end_R - clip_end_R
p_L = p_L[clip_start_L:len(p_L) - clip_end_L]
p_R = p_R[clip_start_R:len(p_R) - clip_end_R]
s_p_L = sum(p_L)
s_p_R = sum(p_R)
p_L = [x / s_p_L for x in p_L]
p_R = [x / s_p_R for x in p_R]
max_i_L = p_L.index(max(p_L))
max_i_R = p_R.index(max(p_R))
ninefive_i_L_start = max_i_L
ninefive_i_L_end = max_i_L
ninefive_i_L_total = p_L[max_i_L]
updated = 0
while (ninefive_i_L_total < 0.95):
if (ninefive_i_L_start <= 0) and (ninefive_i_L_end >=
(len(p_L) - 1)):
break
ninefive_i_L_start = max(0, ninefive_i_L_start - 1)
ninefive_i_L_end = min(len(p_L) - 1, ninefive_i_L_end + 1)
ninefive_i_L_total = sum(p_L[ninefive_i_L_start:ninefive_i_L_end +
1])
ninefive_i_L_start = ninefive_i_L_start - max_i_L
ninefive_i_L_end = ninefive_i_L_end - max_i_L
ninefive_i_R_start = max_i_R
ninefive_i_R_end = max_i_R
ninefive_i_R_total = p_R[max_i_R]
updated = 0
while (ninefive_i_R_total < 0.95):
if (ninefive_i_R_start <= 0) and (ninefive_i_R_end >=
len(p_R) - 1):
break
ninefive_i_R_start = max(0, ninefive_i_R_start - 1)
ninefive_i_R_end = min(len(p_R) - 1, ninefive_i_R_end + 1)
ninefive_i_R_total = sum(p_R[ninefive_i_R_start:ninefive_i_R_end +
1])
ninefive_i_R_end = ninefive_i_R_end - max_i_R
ninefive_i_R_start = ninefive_i_R_start - max_i_R
CIPOS95 = str(ninefive_i_L_start) + ',' + str(ninefive_i_L_end)
CIEND95 = str(ninefive_i_R_start) + ',' + str(ninefive_i_R_end)
CHROM = BP[c[0]].chr_l
POS = new_start_L + max_i_L
v_id += 1
ID = str(v_id)
REF = 'N'
ALT = ''
if BP[c[0]].sv_type == 'BND':
if BP[c[0]].strands[:2] == '++':
ALT = 'N]' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']'
elif BP[c[0]].strands[:2] == '-+':
ALT = ']' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']N'
elif BP[c[0]].strands[:2] == '+-':
ALT = 'N[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'['
elif BP[c[0]].strands[:2] == '--':
ALT = '[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'[N'
else:
ALT = '<' + BP[c[0]].sv_type + '>'
QUAL = 0.0
FILTER = '.'
FORMAT = BP[c[0]].l.split('\t')[8]
SVTYPE = BP[c[0]].sv_type
STRANDS = ''
strand_map = {}
e_type_map = {}
SU = 0
PE = 0
SR = 0
s_name_list = []
gt_list = []
for b_i in c:
A = BP[b_i].l.rstrip().split('\t')
if A[5].isdigit():
QUAL += float(A[5])
m = l_bp.to_map(A[7])
for strand_entry in m['STRANDS'].split(','):
s_type, s_count = strand_entry.split(':')
if s_type not in strand_map:
strand_map[s_type] = 0
strand_map[s_type] += int(s_count)
SU += int(m['SU'])
PE += int(m['PE'])
SR += int(m['SR'])
s_name_list.append(m['SNAME'] + ':' + A[2])
gt_list += A[9:]
SNAME = ','.join(s_name_list)
GTS = '\t'.join(gt_list)
strand_types_counts = []
for strand in strand_map:
strand_types_counts.append(strand + ':' + str(strand_map[strand]))
STRANDS = ','.join(strand_types_counts)
if SVTYPE == 'DEL':
SVLEN = (new_start_L + max_i_L) - (new_start_R + max_i_R)
else:
SVLEN = (new_start_R + max_i_R) - (new_start_L + max_i_L)
# Don't set SVLEN if we have an interchromosomal event. Doesn't make any sense.
if BP[c[0]].chr_l != BP[c[0]].chr_r:
SVLEN = None
END = new_start_R + max_i_R
CIPOS = ','.join(
[str(x)
for x in [-1 * max_i_L, len(p_L) - max_i_L - 1]])
CIEND = ','.join(
[str(x)
for x in [-1 * max_i_R, len(p_R) - max_i_R - 1]])
IMPRECISE = 'IMPRECISE'
PRPOS = ','.join([str(x) for x in p_L])
PREND = ','.join([str(x) for x in p_R])
if (int(CIPOS.split(',')[0]) > int(CIPOS95.split(',')[0])) or \
(int(CIPOS.split(',')[1]) < int(CIPOS95.split(',')[1])) or \
(int(CIEND.split(',')[0]) > int(CIEND95.split(',')[0])) or \
(int(CIEND.split(',')[1]) < int(CIEND95.split(',')[1])):
sys.stderr.write(CIPOS + "\t" + str(CIPOS95) + "\n")
sys.stderr.write(CIEND + "\t" + str(CIEND95) + "\n")
I = ['SVTYPE=' + str(SVTYPE), 'STRANDS=' + str(STRANDS)]
if SVLEN:
I += ['SVLEN=' + str(SVLEN)]
I += [
'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), 'ALG=' + str(ALG),
'SNAME=' + str(SNAME)
]
if BP[c[0]].sv_type == 'BND':
I.append('EVENT=' + str(ID))
else:
I.append('END=' + str(END))
INFO = ';'.join(I)
QUAL = str(QUAL)
O = [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO]
print_var_line('\t'.join([str(o) for o in O]))
return v_id
def combine_pdfs(BP, c, use_product, weighting_scheme):
L = []
R = []
for b_i in c:
b = BP[b_i]
L.append([b.left.start, b.left.end, b.left.p])
R.append([b.right.start, b.right.end, b.right.p])
[start_R, end_R, a_R] = l_bp.align_intervals(R)
[start_L, end_L, a_L] = l_bp.align_intervals(L)
p_L = [0] * len(a_L[0])
p_R = [0] * len(a_R[0])
wts = [1] * len(c)
for c_i in range(len(c)):
if weighting_scheme == 'evidence_wt':
A = BP[c[c_i]].l.rstrip().split('\t', 10)
m = l_bp.to_map(A[7])
wt=int(m['SU'])
#sys.stderr.write("wt\t0\t"+str(wt)+"\n")
a_L[c_i]=[wt*ali for ali in a_L[c_i]]
a_R[c_i]=[wt*ari for ari in a_R[c_i]]
elif weighting_scheme == 'carrier_wt':
A = BP[c[c_i]].l.rstrip().split('\t', 10)
m = l_bp.to_map(A[7])
wt = 1
if 'SNAME' in m:
wt=len(m['SNAME'].split(','))
a_L[c_i]=[wt*ali for ali in a_L[c_i]]
a_R[c_i]=[wt*ari for ari in a_R[c_i]]
for i in range(len(a_L[c_i])):
#sys.stderr.write("L\t"+str(i)+"\t"+str(c_i)+"\t"+str(a_L[c_i][i])+"\n")
p_L[i] += a_L[c_i][i]
for i in range(len(a_R[c_i])):
#sys.stderr.write("R\t"+str(i)+"\t"+str(c_i)+"\t"+str(a_R[c_i][i])+"\n")
p_R[i] += a_R[c_i][i]
ALG = 'SUM'
if use_product:
pmax_i_L = p_L.index(max(p_L))
pmax_i_R = p_R.index(max(p_R))
miss = 0
for c_i in range(len(c)):
if (a_L[c_i][pmax_i_L] == 0) or (a_R[c_i][pmax_i_R] == 0):
miss += 1
if miss == 0:
ALG = "PROD"
ls_p_L = [ls.get_ls(1)] * len(a_L[0])
ls_p_R = [ls.get_ls(1)] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
ls_p_L[i] = ls.ls_multiply(ls_p_L[i], ls.get_ls(a_L[c_i][i]))
for i in range(len(a_R[c_i])):
ls_p_R[i] = ls.ls_multiply(ls_p_R[i], ls.get_ls(a_R[c_i][i]))
ls_sum_L = ls.get_ls(0)
ls_sum_R = ls.get_ls(0)
for ls_p in ls_p_L:
ls_sum_L = ls.ls_add(ls_sum_L, ls_p)
for ls_p in ls_p_R:
ls_sum_R = ls.ls_add(ls_sum_R, ls_p)
p_L = []
for ls_p in ls_p_L:
p_L.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_L)))
p_R = []
for ls_p in ls_p_R:
p_R.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_R)))
sum_L = sum(p_L)
sum_R = sum(p_R)
p_L = [x/sum_L for x in p_L]
p_R = [x/sum_L for x in p_R]
[clip_start_L, clip_end_L] = l_bp.trim(p_L)
[clip_start_R, clip_end_R] = l_bp.trim(p_R)
[ new_start_L, new_end_L ] = [ start_L + clip_start_L, end_L - clip_end_L ]
[ new_start_R, new_end_R ] = [ start_R + clip_start_R, end_R - clip_end_R ]
p_L = p_L[clip_start_L:len(p_L)-clip_end_L]
p_R = p_R[clip_start_R:len(p_R)-clip_end_R]
s_p_L = sum(p_L)
s_p_R = sum(p_R)
p_L = [x/s_p_L for x in p_L]
p_R = [x/s_p_R for x in p_R]
#sys.exit(1)
return new_start_L, new_start_R, p_L, p_R, ALG
def merge(BP, sample_order, v_id, use_product):
if len(BP) == 1:
A = BP[0].l.rstrip().split('\t')
#tack on id to SNAME
s_start=A[7].find('SNAME=')
s_end=A[7].find(';',s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + \
A[7][s_start:s_end] + \
':' + A[2] + \
A[7][s_end:]
else:
A[7]+= ':' + A[2]
# reset the id to be unique in this file
v_id += 1
A[2] = str(v_id)
#clip out old mate id
s_start=A[7].find('MATEID=')
s_end=A[7].find(';',s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end+1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#clip out old event id
s_start=A[7].find('EVENT=')
s_end=A[7].find(';', s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end+1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#add new mate
A[7]+= ';EVENT=' + A[2]
#add new alg
if use_product:
A[7]+= ';ALG=PROD'
else:
A[7] += ';ALG=SUM'
print_var_line('\t'.join(A))
return v_id
#Sweep the set. Find the largest intersecting set. Remove it. Continue.
import heapq
BP.sort(key=lambda x: x.start_l)
BP_i = range(len(BP))
C = []
while len(BP_i) > 0:
h_l = []
max_c = []
max_c_len = 0
for i in BP_i:
while (len(h_l) > 0) and (h_l[0][0] < BP[i].start_l):
heapq.heappop(h_l)
heapq.heappush(h_l, (BP[i].end_l, i))
# at this point everything in h_l intersects on the left
# but we need to take into account what is going on on the right
h_r = []
h_l_i = [x[1] for x in h_l]
h_l_i.sort(key=lambda x:BP[x].start_r)
for j in h_l_i:
while (len(h_r) > 0) and (h_r[0][0] < BP[j].start_r):
heapq.heappop(h_r)
heapq.heappush(h_r, (BP[j].end_r, j))
if max_c_len < len(h_r):
max_c_len = len(h_r)
max_c = [y[1] for y in h_r]
C.append(max_c)
for c in max_c:
BP_i.remove(c)
for c in C:
L = []
R = []
for b_i in c:
b = BP[b_i]
L.append([b.start_l,b.end_l,b.p_l])
R.append([b.start_r,b.end_r,b.p_r])
[start_R, end_R, a_R] = l_bp.align_intervals(R)
[start_L, end_L, a_L] = l_bp.align_intervals(L)
p_L = [0] * len(a_L[0])
p_R = [0] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
p_L[i] += a_L[c_i][i]
for i in range(len(a_R[c_i])):
p_R[i] += a_R[c_i][i]
ALG = 'SUM'
if use_product:
pmax_i_L = p_L.index(max(p_L))
pmax_i_R = p_R.index(max(p_R))
miss = 0
for c_i in range(len(c)):
if (a_L[c_i][pmax_i_L] == 0) or (a_R[c_i][pmax_i_R] == 0):
miss += 1
if miss == 0:
ALG = "PROD"
ls_p_L = [get_ls(1)] * len(a_L[0])
ls_p_R = [get_ls(1)] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
ls_p_L[i] = ls_multiply(ls_p_L[i], get_ls(a_L[c_i][i]))
for i in range(len(a_R[c_i])):
ls_p_R[i] = ls_multiply(ls_p_R[i], get_ls(a_R[c_i][i]))
ls_sum_L = get_ls(0)
ls_sum_R = get_ls(0)
for ls_p in ls_p_L:
ls_sum_L = ls_add(ls_sum_L, ls_p)
for ls_p in ls_p_R:
ls_sum_R = ls_add(ls_sum_R, ls_p)
p_L = []
for ls_p in ls_p_L:
p_L.append(get_p(ls_divide(ls_p, ls_sum_L)))
p_R = []
for ls_p in ls_p_R:
p_R.append(get_p(ls_divide(ls_p, ls_sum_R)))
sum_L = sum(p_L)
sum_R = sum(p_R)
p_L = [x/sum_L for x in p_L]
p_R = [x/sum_L for x in p_R]
[clip_start_L, clip_end_L] = l_bp.trim(p_L)
[clip_start_R, clip_end_R] = l_bp.trim(p_R)
new_start_L = start_L + clip_start_L
new_end_L = end_L - clip_end_L
new_start_R = start_R + clip_start_R
new_end_R = end_R - clip_end_R
p_L = p_L[clip_start_L:len(p_L)-clip_end_L]
p_R = p_R[clip_start_R:len(p_R)-clip_end_R]
s_p_L = sum(p_L)
s_p_R = sum(p_R)
p_L = [x/s_p_L for x in p_L]
p_R = [x/s_p_R for x in p_R]
max_i_L = p_L.index(max(p_L))
max_i_R = p_R.index(max(p_R))
ninefive_i_L_start = max_i_L
ninefive_i_L_end = max_i_L
ninefive_i_L_total = p_L[max_i_L]
updated = 0
while (ninefive_i_L_total < 0.95):
if (ninefive_i_L_start <= 0) and (ninefive_i_L_end >= (len(p_L)-1)):
break
ninefive_i_L_start = max(0, ninefive_i_L_start - 1)
ninefive_i_L_end = min(len(p_L)-1, ninefive_i_L_end +1)
ninefive_i_L_total = sum(p_L[ninefive_i_L_start:ninefive_i_L_end+1])
ninefive_i_L_start = ninefive_i_L_start - max_i_L
ninefive_i_L_end = ninefive_i_L_end - max_i_L
ninefive_i_R_start = max_i_R
ninefive_i_R_end = max_i_R
ninefive_i_R_total = p_R[max_i_R]
updated = 0
while (ninefive_i_R_total < 0.95):
if (ninefive_i_R_start <= 0) and (ninefive_i_R_end >= len(p_R)-1):
break
ninefive_i_R_start = max(0, ninefive_i_R_start - 1)
ninefive_i_R_end = min(len(p_R)-1, ninefive_i_R_end +1)
ninefive_i_R_total = sum(p_R[ninefive_i_R_start:ninefive_i_R_end+1])
ninefive_i_R_end = ninefive_i_R_end - max_i_R
ninefive_i_R_start = ninefive_i_R_start - max_i_R
CIPOS95=str(ninefive_i_L_start) + ',' + str(ninefive_i_L_end)
CIEND95=str(ninefive_i_R_start) + ',' + str(ninefive_i_R_end)
CHROM = BP[c[0]].chr_l
POS = new_start_L + max_i_L
v_id += 1
ID = str(v_id)
REF = 'N'
ALT = ''
if BP[c[0]].sv_type == 'BND':
if BP[c[0]].strands[:2] == '++':
ALT = 'N]' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']'
elif BP[c[0]].strands[:2] == '-+':
ALT = ']' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']N'
elif BP[c[0]].strands[:2] == '+-':
ALT = 'N[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'['
elif BP[c[0]].strands[:2] == '--':
ALT = '[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'[N'
else:
ALT = '<' + BP[c[0]].sv_type + '>'
QUAL = 0.0
FILTER = '.'
FORMAT = BP[c[0]].l.split('\t')[8]
SVTYPE = BP[c[0]].sv_type
STRANDS = ''
strand_map = {}
e_type_map = {}
SU = 0
PE = 0
SR = 0
s_name_list = []
gt_list = []
for b_i in c:
A = BP[b_i].l.rstrip().split('\t')
if A[5].isdigit():
QUAL += float(A[5])
m = l_bp.to_map(A[7])
for strand_entry in m['STRANDS'].split(','):
s_type,s_count = strand_entry.split(':')
if s_type not in strand_map:
strand_map[s_type] = 0
strand_map[s_type] += int(s_count)
SU += int(m['SU'])
PE += int(m['PE'])
SR += int(m['SR'])
s_name_list.append(m['SNAME'] + ':' + A[2])
gt_list += A[9:]
SNAME=','.join(s_name_list)
GTS = '\t'.join(gt_list)
strand_types_counts = []
for strand in strand_map:
strand_types_counts.append(strand + ':' + str(strand_map[strand]))
STRANDS = ','.join(strand_types_counts)
if SVTYPE=='DEL':
SVLEN = (new_start_L + max_i_L) - (new_start_R + max_i_R)
else:
SVLEN = (new_start_R + max_i_R) - (new_start_L + max_i_L)
END = new_start_R + max_i_R
CIPOS=','.join([str(x) for x in [-1*max_i_L, len(p_L) - max_i_L - 1]])
CIEND=','.join([str(x) for x in [-1*max_i_R, len(p_R) - max_i_R - 1]])
IMPRECISE='IMPRECISE'
PRPOS=','.join([str(x) for x in p_L])
PREND=','.join([str(x) for x in p_R])
if (int(CIPOS.split(',')[0]) > int(CIPOS95.split(',')[0])) or \
(int(CIPOS.split(',')[1]) < int(CIPOS95.split(',')[1])) or \
(int(CIEND.split(',')[0]) > int(CIEND95.split(',')[0])) or \
(int(CIEND.split(',')[1]) < int(CIEND95.split(',')[1])):
sys.stderr.write(CIPOS + "\t" + str(CIPOS95) + "\n")
sys.stderr.write(CIEND + "\t" + str(CIEND95) + "\n")
I = ['SVTYPE=' + str(SVTYPE),
'STRANDS=' + str(STRANDS),
'SVLEN=' + str(SVLEN),
'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),
'ALG=' + str(ALG),
'SNAME=' + str(SNAME)]
if BP[c[0]].sv_type == 'BND':
I.append('EVENT=' + str(ID))
else:
I.append('END=' + str(END))
INFO = ';'.join(I)
QUAL = str(QUAL)
O = [CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO]
print_var_line('\t'.join([str(o) for o in O]))
return v_id
def merge(BP, sample_order, v_id, use_product, include_genotypes=False):
if len(BP) == 1:
A = BP[0].l.rstrip().split('\t')
#tack on id to SNAME
s_start=A[7].find('SNAME=')
s_end=A[7].find(';',s_start)
sname = None
if (s_end > -1):
sname = A[7][s_start + 6:s_end]
A[7] = A[7][:s_start] + \
A[7][s_start:s_end] + \
':' + A[2] + \
A[7][s_end:]
else:
sname = A[7][s_start + 6:]
A[7]+= ':' + A[2]
# reset the id to be unique in this file
v_id += 1
A[2] = str(v_id)
#clip out old mate id
s_start=A[7].find('MATEID=')
s_end=A[7].find(';',s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end+1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#clip out old event id
s_start=A[7].find('EVENT=')
s_end=A[7].find(';', s_start)
if (s_end > -1):
A[7] = A[7][:s_start] + A[7][s_end+1:]
elif (s_start > -1):
A[7] = A[7][:s_start]
#add new mate
A[7]+= ';EVENT=' + A[2]
#add new alg
if use_product:
A[7]+= ';ALG=PROD'
else:
A[7] += ';ALG=SUM'
GTS = None
if include_genotypes:
null_string = null_format_string(A[8])
gt_dict = { sname: A[9] }
GTS = '\t'.join([A[8]] + [gt_dict.get(x, null_string) for x in sample_order])
print_var_line('\t'.join(A), GTS)
return v_id
#Sweep the set. Find the largest intersecting set. Remove it. Continue.
import heapq
BP.sort(key=lambda x: x.start_l)
BP_i = range(len(BP)) # index set of each node in the graph
C = []
while len(BP_i) > 0:
h_l = [] #heap of left breakpoint end coordinates and node id (index). heapq is a min heap and the end coord is what will be used for the sorting.
max_c = []
max_c_len = 0
for i in BP_i:
# remove anything in the heap that doesn't intersect with the current breakpoint
while (len(h_l) > 0) and (h_l[0][0] < BP[i].start_l):
heapq.heappop(h_l)
heapq.heappush(h_l, (BP[i].end_l, i)) # add to the heap
# at this point everything in h_l intersects on the left
# but we need to take into account what is going on on the right
h_r = [] # heap with rightmost starts
h_l_i = [x[1] for x in h_l] # this is all of the node ids on the heap currently
h_l_i.sort(key=lambda x:BP[x].start_r) # sort them by their right start
for j in h_l_i:
# remove anything in the heap that doesn't intersect with the current breakpoint on the right end
while (len(h_r) > 0) and (h_r[0][0] < BP[j].start_r):
heapq.heappop(h_r)
# add something to the right heap
heapq.heappush(h_r, (BP[j].end_r, j))
if max_c_len < len(h_r):
# max clique! Register what nodes we have
max_c_len = len(h_r)
max_c = [y[1] for y in h_r]
C.append(max_c)
for c in max_c:
BP_i.remove(c)
for c in C:
L = []
R = []
for b_i in c:
b = BP[b_i]
L.append([b.start_l,b.end_l,b.p_l])
R.append([b.start_r,b.end_r,b.p_r])
[start_R, end_R, a_R] = l_bp.align_intervals(R)
[start_L, end_L, a_L] = l_bp.align_intervals(L)
p_L = [0] * len(a_L[0])
p_R = [0] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
p_L[i] += a_L[c_i][i]
for i in range(len(a_R[c_i])):
p_R[i] += a_R[c_i][i]
ALG = 'SUM'
if use_product:
pmax_i_L = p_L.index(max(p_L))
pmax_i_R = p_R.index(max(p_R))
miss = 0
for c_i in range(len(c)):
if (a_L[c_i][pmax_i_L] == 0) or (a_R[c_i][pmax_i_R] == 0):
miss += 1
if miss == 0:
ALG = "PROD"
ls_p_L = [ls.get_ls(1)] * len(a_L[0])
ls_p_R = [ls.get_ls(1)] * len(a_R[0])
for c_i in range(len(c)):
for i in range(len(a_L[c_i])):
ls_p_L[i] = ls.ls_multiply(ls_p_L[i], ls.get_ls(a_L[c_i][i]))
for i in range(len(a_R[c_i])):
ls_p_R[i] = ls.ls_multiply(ls_p_R[i], ls.get_ls(a_R[c_i][i]))
ls_sum_L = ls.get_ls(0)
ls_sum_R = ls.get_ls(0)
for ls_p in ls_p_L:
ls_sum_L = ls.ls_add(ls_sum_L, ls_p)
for ls_p in ls_p_R:
ls_sum_R = ls.ls_add(ls_sum_R, ls_p)
p_L = []
for ls_p in ls_p_L:
p_L.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_L)))
p_R = []
for ls_p in ls_p_R:
p_R.append(ls.get_p(ls.ls_divide(ls_p, ls_sum_R)))
sum_L = sum(p_L)
sum_R = sum(p_R)
p_L = [x/sum_L for x in p_L]
p_R = [x/sum_L for x in p_R]
[clip_start_L, clip_end_L] = l_bp.trim(p_L)
[clip_start_R, clip_end_R] = l_bp.trim(p_R)
new_start_L = start_L + clip_start_L
new_end_L = end_L - clip_end_L
new_start_R = start_R + clip_start_R
new_end_R = end_R - clip_end_R
p_L = p_L[clip_start_L:len(p_L)-clip_end_L]
p_R = p_R[clip_start_R:len(p_R)-clip_end_R]
s_p_L = sum(p_L)
s_p_R = sum(p_R)
p_L = [x/s_p_L for x in p_L]
p_R = [x/s_p_R for x in p_R]
max_i_L = p_L.index(max(p_L))
max_i_R = p_R.index(max(p_R))
ninefive_i_L_start = max_i_L
ninefive_i_L_end = max_i_L
ninefive_i_L_total = p_L[max_i_L]
updated = 0
while (ninefive_i_L_total < 0.95):
if (ninefive_i_L_start <= 0) and (ninefive_i_L_end >= (len(p_L)-1)):
break
ninefive_i_L_start = max(0, ninefive_i_L_start - 1)
ninefive_i_L_end = min(len(p_L)-1, ninefive_i_L_end +1)
ninefive_i_L_total = sum(p_L[ninefive_i_L_start:ninefive_i_L_end+1])
ninefive_i_L_start = ninefive_i_L_start - max_i_L
ninefive_i_L_end = ninefive_i_L_end - max_i_L
ninefive_i_R_start = max_i_R
ninefive_i_R_end = max_i_R
ninefive_i_R_total = p_R[max_i_R]
updated = 0
while (ninefive_i_R_total < 0.95):
if (ninefive_i_R_start <= 0) and (ninefive_i_R_end >= len(p_R)-1):
break
ninefive_i_R_start = max(0, ninefive_i_R_start - 1)
ninefive_i_R_end = min(len(p_R)-1, ninefive_i_R_end +1)
ninefive_i_R_total = sum(p_R[ninefive_i_R_start:ninefive_i_R_end+1])
ninefive_i_R_end = ninefive_i_R_end - max_i_R
ninefive_i_R_start = ninefive_i_R_start - max_i_R
CIPOS95=str(ninefive_i_L_start) + ',' + str(ninefive_i_L_end)
CIEND95=str(ninefive_i_R_start) + ',' + str(ninefive_i_R_end)
CHROM = BP[c[0]].chr_l
POS = new_start_L + max_i_L
v_id += 1
ID = str(v_id)
REF = 'N'
ALT = ''
if BP[c[0]].sv_type == 'BND':
if BP[c[0]].strands[:2] == '++':
ALT = 'N]' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']'
elif BP[c[0]].strands[:2] == '-+':
ALT = ']' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
']N'
elif BP[c[0]].strands[:2] == '+-':
ALT = 'N[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'['
elif BP[c[0]].strands[:2] == '--':
ALT = '[' + \
BP[c[0]].chr_r + \
':' + \
str(new_start_R + max_i_R) + \
'[N'
else:
ALT = '<' + BP[c[0]].sv_type + '>'
QUAL = 0.0
FILTER = '.'
FORMAT = BP[c[0]].l.split('\t')[8]
SVTYPE = BP[c[0]].sv_type
STRANDS = ''
strand_map = {}
e_type_map = {}
SU = 0
PE = 0
SR = 0
s_name_list = []
format_string = None
gt_dict = dict()
for b_i in c:
A = BP[b_i].l.rstrip().split('\t')
if A[5].isdigit():
QUAL += float(A[5])
m = l_bp.to_map(A[7])
for strand_entry in m['STRANDS'].split(','):
s_type,s_count = strand_entry.split(':')
if s_type not in strand_map:
strand_map[s_type] = 0
strand_map[s_type] += int(s_count)
SU += int(m['SU'])
PE += int(m['PE'])
SR += int(m['SR'])
s_name_list.append(m['SNAME'] + ':' + A[2])
if include_genotypes:
if format_string == None:
format_string = A[8]
if format_string == A[8]:
gt_dict[m['SNAME']] = A[9]
else:
longer = A[8]
shorter = format_string
if len(longer) < len(shorter):
longer, shorter = shorter, longer
if longer.find(shorter) == 0:
format_string = longer
gt_dict[m['SNAME']] = A[9]
else:
sys.stderr.write('Unable to merge and include genotypes when FORMAT fields differ across VCF files\n')
sys.stderr.write('Previous: {0} Current: {1}\n'.format(format_string, A[8]))
sys.stderr.write('Variant: {0}\n'.format(m['SNAME'] + ':' + A[2]))
sys.exit(1)
SNAME=','.join(s_name_list)
GTS = None
if include_genotypes:
null_string = null_format_string(format_string)
GTS = '\t'.join([format_string] + [gt_dict.get(x, null_string) for x in sample_order])
strand_types_counts = []
for strand in strand_map:
strand_types_counts.append(strand + ':' + str(strand_map[strand]))
STRANDS = ','.join(strand_types_counts)
if SVTYPE=='DEL':
SVLEN = (new_start_L + max_i_L) - (new_start_R + max_i_R)
else:
SVLEN = (new_start_R + max_i_R) - (new_start_L + max_i_L)
# Don't set SVLEN if we have an interchromosomal event. Doesn't make any sense.
if BP[c[0]].chr_l != BP[c[0]].chr_r:
SVLEN = None
END = new_start_R + max_i_R
CIPOS=','.join([str(x) for x in [-1*max_i_L, len(p_L) - max_i_L - 1]])
CIEND=','.join([str(x) for x in [-1*max_i_R, len(p_R) - max_i_R - 1]])
IMPRECISE='IMPRECISE'
PRPOS=','.join([str(x) for x in p_L])
PREND=','.join([str(x) for x in p_R])
if (int(CIPOS.split(',')[0]) > int(CIPOS95.split(',')[0])) or \
(int(CIPOS.split(',')[1]) < int(CIPOS95.split(',')[1])) or \
(int(CIEND.split(',')[0]) > int(CIEND95.split(',')[0])) or \
(int(CIEND.split(',')[1]) < int(CIEND95.split(',')[1])):
sys.stderr.write(CIPOS + "\t" + str(CIPOS95) + "\n")
sys.stderr.write(CIEND + "\t" + str(CIEND95) + "\n")
I = ['SVTYPE=' + str(SVTYPE),
'STRANDS=' + str(STRANDS)
]
if SVLEN is not None:
I += ['SVLEN=' + str(SVLEN)]
I += ['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),
'ALG=' + str(ALG),
'SNAME=' + str(SNAME)]
if BP[c[0]].sv_type == 'BND':
I.append('EVENT=' + str(ID))
else:
I.append('END=' + str(END))
INFO = ';'.join(I)
QUAL = str(QUAL)
O = [CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO]
print_var_line('\t'.join([str(o) for o in O]), GTS)
return v_id