def generate_pvcf(args, result, contigINFO, argv):
file = open(args.output, 'w')
Generation_VCF_header(file, contigINFO, args.sample, argv)
file.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n" %
(args.sample))
for i in result:
if i == []:
continue
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES};STRAND={STRAND}".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[5],
CIPOS=i[6][0] + ',' + i[6][1],
CILEN=i[7][0] + ',' + i[7][1],
RE=i[8],
RNAMES=i[9] if args.report_readid else "NULL",
STRAND=i[14])
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=i[11],
ALT=i[12],
QUAL='.' if i[13] == None else i[13],
PASS='******' if i[15] == [] else i[15],
INFO=info_list,
FORMAT="GT",
GT=i[2]))
def generate_pvcf(args, result, contigINFO, argv, ref_g):
file = open(args.output, 'w')
Generation_VCF_header(file, contigINFO, args.sample, argv)
file.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n" %
(args.sample))
for i in result:
if i == []:
continue
if i[13] == "." or i[13] == None:
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[13]) >= 5.0 else "q5"
if i[3] == 'INS':
if abs(i[4]) > args.max_size and args.max_size != -1:
continue
elif i[12] == '<INS>':
ref = str(ref_g[i[0]].seq[max(i[1] - 1, 0)])
alt = str(ref_g[i[0]].seq[max(i[1] - 1, 0)]) + i[15]
else:
ref = i[11]
alt = i[12]
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[1],
CIPOS=i[6],
CILEN=i[7],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
try:
info_list += ";AF=" + str(
round(i[8][0] / (i[8][0] + i[8][1]), 4))
except:
info_list += ";AF=."
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=ref,
ALT=alt,
QUAL=i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))
elif i[3] == 'DEL':
if abs(i[4]) > args.max_size and args.max_size != -1:
continue
elif i[12] == '<DEL>':
ref = str(ref_g[i[0]].seq[max(int(i[1]) - 1, 0):int(i[1]) -
int(i[4])])
alt = str(ref_g[i[0]].seq[max(int(i[1]) - 1, 0)])
else:
ref = i[11]
alt = i[12]
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES};STRAND=+-".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[1] + abs(i[4]),
CIPOS=i[6],
CILEN=i[7],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
try:
info_list += ";AF=" + str(
round(i[8][0] / (i[8][0] + i[8][1]), 4))
except:
info_list += ";AF=."
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=ref,
ALT=alt,
QUAL=i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))
elif i[3] == 'DUP':
if abs(i[4]) > args.max_size and args.max_size != -1:
continue
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND=-+".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[5],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
try:
info_list += ";AF=" + str(
round(i[8][0] / (i[8][0] + i[8][1]), 4))
except:
info_list += ";AF=."
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=i[11],
ALT=i[12],
QUAL=i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))
elif i[3] == 'INV':
if abs(i[4]) > args.max_size and args.max_size != -1:
continue
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND={STRAND}".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[5],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL",
STRAND=i[14])
try:
info_list += ";AF=" + str(
round(i[8][0] / (i[8][0] + i[8][1]), 4))
except:
info_list += ";AF=."
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=i[11],
ALT=i[12],
QUAL=i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))
else:
# BND
info_list = "{PRECISION};SVTYPE={SVTYPE};RE={RE};RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
try:
info_list += ";AF=" + str(
round(i[8][0] / (i[8][0] + i[8][1]), 4))
except:
info_list += ";AF=."
if ':' in i[15]:
info_list += ";CHR2={CHR2};END={END}".format(
CHR2=i[15].split(':')[0], END=i[15].split(':')[1])
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=i[11],
ALT=i[12],
QUAL=i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))
def generate_output(args, semi_result, contigINFO, argv, ref_g):
'''
Generation of VCF format file.
VCF version: 4.2
'''
# genotype_trigger = TriggerGT[args.genotype]
svid = dict()
svid["INS"] = 0
svid["DEL"] = 0
svid["BND"] = 0
svid["DUP"] = 0
svid["INV"] = 0
file = open(args.output, 'w')
action = args.genotype
Generation_VCF_header(file, contigINFO, args.sample, argv)
file.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n" %
(args.sample))
for i in semi_result:
if i[1] in ["DEL", "INS"]:
if abs(int(float(i[3]))) > args.max_size and args.max_size != -1:
continue
if i[1] == "INS":
cal_end = int(i[2])
else:
cal_end = int(i[2]) + abs(int(float(i[3])))
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[8] == "0/0" else "PRECISE",
SVTYPE=i[1],
SVLEN=i[3],
END=str(cal_end),
CIPOS=i[5],
CILEN=i[6],
RE=i[4],
RNAMES=i[12] if args.report_readid else "NULL")
if action:
try:
info_list += ";AF=" + str(
round(int(i[4]) / (int(i[4]) + int(i[7])), 4))
except:
info_list += ";AF=."
if i[1] == "DEL":
info_list += ";STRAND=+-"
if i[11] == "." or i[11] == None:
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[11]) >= 5.0 else "q5"
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(
CHR=i[0],
POS=str(int(i[2])),
ID="cuteSV.%s.%d" % (i[1], svid[i[1]]),
REF=str(ref_g[i[0]].seq[max(int(i[2]) - 1, 0)]) if i[1]
== 'INS' else str(ref_g[i[0]].seq[max(int(i[2]) -
1, 0):int(i[2]) -
int(i[3])]),
ALT="%s" % (str(ref_g[i[0]].seq[max(int(i[2]) - 1, 0)]) +
i[13] if i[1] == 'INS' else str(
ref_g[i[0]].seq[max(int(i[2]) - 1, 0)])),
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[8],
DR=i[7],
RE=i[4],
PL=i[9],
GQ=i[10],
QUAL=i[11],
PASS=filter_lable))
svid[i[1]] += 1
elif i[1] == "DUP":
if abs(int(float(i[3]))) > args.max_size and args.max_size != -1:
continue
cal_end = int(i[2]) + 1 + abs(int(float(i[3])))
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};STRAND=-+;RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[6] == "0/0" else "PRECISE",
SVTYPE=i[1],
SVLEN=i[3],
END=str(cal_end),
RE=i[4],
RNAMES=i[10] if args.report_readid else "NULL")
if action:
try:
info_list += ";AF=" + str(
round(int(i[4]) / (int(i[4]) + int(i[5])), 4))
except:
info_list += ";AF=."
if i[9] == ".":
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[9]) >= 5.0 else "q5"
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(int(i[2]) + 1),
ID="cuteSV.%s.%d" % (i[1], svid[i[1]]),
REF=str(ref_g[i[0]].seq[int(i[2])]),
ALT="<%s>" % (i[1]),
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[6],
DR=i[5],
RE=i[4],
PL=i[7],
GQ=i[8],
QUAL=i[9],
PASS=filter_lable))
svid[i[1]] += 1
elif i[1] == "INV":
if abs(int(float(i[3]))) > args.max_size and args.max_size != -1:
continue
cal_end = int(i[2]) + 1 + abs(int(float(i[3])))
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};STRAND={STRAND};RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[6] == "0/0" else "PRECISE",
SVTYPE=i[1],
SVLEN=i[3],
END=str(cal_end),
RE=i[4],
STRAND=i[7],
RNAMES=i[11] if args.report_readid else "NULL")
if action:
try:
info_list += ";AF=" + str(
round(int(i[4]) / (int(i[4]) + int(i[5])), 4))
except:
info_list += ";AF=."
if i[10] == ".":
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[10]) >= 5.0 else "q5"
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(int(i[2]) + 1),
ID="cuteSV.%s.%d" % (i[1], svid[i[1]]),
REF=str(ref_g[i[0]].seq[int(i[2])]),
ALT="<%s>" % (i[1]),
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[6],
DR=i[5],
RE=i[4],
PL=i[8],
GQ=i[9],
QUAL=i[10],
PASS=filter_lable))
svid[i[1]] += 1
else:
# BND
# info_list = "{PRECISION};SVTYPE={SVTYPE};CHR2={CHR2};END={END};RE={RE};RNAMES={RNAMES}".format(
info_list = "{PRECISION};SVTYPE={SVTYPE};RE={RE};RNAMES={RNAMES}".format(
PRECISION="IMPRECISE" if i[7] == "0/0" else "PRECISE",
SVTYPE="BND",
# CHR2 = i[3],
# END = str(int(i[4]) + 1),
RE=i[5],
RNAMES=i[11] if args.report_readid else "NULL")
if action:
try:
info_list += ";AF=" + str(
round(int(i[5]) / (int(i[5]) + int(i[6])), 4))
except:
info_list += ";AF=."
if i[10] == ".":
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[10]) >= 5.0 else "q5"
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(int(i[2]) + 1),
ID="cuteSV.%s.%d" % ("BND", svid["BND"]),
REF='N',
ALT=i[1],
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[7],
DR=i[6],
RE=i[5],
PL=i[8],
GQ=i[9],
QUAL=i[10],
PASS=filter_lable))
svid["BND"] += 1
def generate_pvcf(args, result, contigINFO, argv):
file = open(args.output, 'w')
Generation_VCF_header(file, contigINFO, args.sample, argv)
file.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n" %
(args.sample))
for i in result:
if i == []:
continue
if i[3] == 'INS':
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES};".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[1],
CIPOS=str(i[6][0]) + ',' + str(i[6][1]),
CILEN=str(i[7][0]) + ',' + str(i[7][1]),
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
elif i[3] == 'DEL':
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};CIPOS={CIPOS};CILEN={CILEN};RE={RE};RNAMES={RNAMES};STRAND=+-".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[1] + abs(i[4]),
CIPOS=str(i[6][0]) + ',' + str(i[6][1]),
CILEN=str(i[7][0]) + ',' + str(i[7][1]),
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
elif i[3] == 'DUP':
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND=-+".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[5],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
elif i[3] == 'INV':
info_list = "{PRECISION};SVTYPE={SVTYPE};SVLEN={SVLEN};END={END};RE={RE};RNAMES={RNAMES};STRAND={STRAND}".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
SVLEN=i[4],
END=i[5],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL",
STRAND=i[14])
else:
# BND
info_list = "{PRECISION};SVTYPE={SVTYPE};RE={RE};RNAMES={RNAMES};".format(
PRECISION="IMPRECISE" if i[2] == "0/0" else "PRECISE",
SVTYPE=i[3],
RE=i[8][0],
RNAMES=i[9] if args.report_readid else "NULL")
if i[13] == "." or i[13] == None:
filter_lable = "PASS"
else:
filter_lable = "PASS" if float(i[13]) >= 5.0 else "q5"
file.write(
"{CHR}\t{POS}\t{ID}\t{REF}\t{ALT}\t{QUAL}\t{PASS}\t{INFO}\t{FORMAT}\t{GT}:{DR}:{RE}:{PL}:{GQ}\n"
.format(CHR=i[0],
POS=str(i[1]),
ID=i[10],
REF=i[11],
ALT=i[12],
QUAL='.' if i[13] == None else i[13],
PASS=filter_lable,
INFO=info_list,
FORMAT="GT:DR:DV:PL:GQ",
GT=i[2],
DR=i[8][1],
RE=i[8][0],
PL=i[8][2],
GQ=i[8][3]))