def rmdup_main(args):
if os.path.getsize(args.fusion) == 0:
hOUT = open(args.output, 'w')
hOUT.close()
return
process.convert_to_bedpe(args.fusion, args.output + ".fusion.bedpe", 10,
10, args.type)
hOUT = open(args.output + ".fusion_comp.bedpe", 'w')
subprocess.check_call([
"bedtools", "pairtopair", "-a", args.output + ".fusion.bedpe", "-b",
args.output + ".fusion.bedpe"
],
stdout=hOUT)
hOUT.close()
# create dictionary
fusion_comp = {}
hIN = open(args.output + ".fusion_comp.bedpe", 'r')
for line in hIN:
F = line.rstrip('\n').split('\t')
if F[6] != F[16]:
if int(F[7]) < int(F[17]) or (int(F[7]) == int(F[17])
and F[6] not in fusion_comp):
fusion_comp[F[6]] = F[16]
hIN.close()
hIN = open(args.fusion, 'r')
hOUT = open(args.output, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
# header is removed
if F[0] == "#fusion_name" and args.type == "star_fusion": continue
chr1, pos1, dir1, chr2, pos2, dir2 = process.get_position(F, args.type)
ID = chr1 + ':' + dir1 + pos1 + '-' + chr2 + ':' + dir2 + pos2
if ID not in fusion_comp:
print >> hOUT, '\t'.join(F)
hIN.close()
hOUT.close()
# remove intermediate files
subprocess.check_call(["rm", "-rf", args.output + ".fusion.bedpe"])
subprocess.check_call(["rm", "-rf", args.output + ".fusion_comp.bedpe"])
def rmdup_main(args):
if os.path.getsize(args.fusion) == 0:
hOUT = open(args.output, 'w')
hOUT.close()
return
process.convert_to_bedpe(args.fusion, args.output + ".fusion.bedpe", 10, 10, args.type)
hOUT = open(args.output + ".fusion_comp.bedpe", 'w')
subprocess.call([args.bedtools_path + "/bedtools", "pairtopair", "-a", args.output + ".fusion.bedpe", "-b", args.output + ".fusion.bedpe"], stdout = hOUT)
hOUT.close()
# create dictionary
fusion_comp = {}
hIN = open(args.output + ".fusion_comp.bedpe", 'r')
for line in hIN:
F = line.rstrip('\n').split('\t')
if F[6] != F[16]:
if int(F[7]) < int(F[17]) or (int(F[7]) == int(F[17]) and F[6] not in fusion_comp):
fusion_comp[F[6]] = F[16]
hIN.close()
hIN = open(args.fusion, 'r')
hOUT = open(args.output, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
# header is removed
if F[0] == "#fusion_name" and args.type == "star_fusion": continue
chr1, pos1, dir1, chr2, pos2, dir2 = process.get_position(F, args.type)
ID = chr1 + ':' + dir1 + pos1 + '-' + chr2 + ':' + dir2 + pos2
if ID not in fusion_comp:
print >> hOUT, '\t'.join(F)
hIN.close()
hOUT.close()
# remove intermediate files
subprocess.call(["rm", "-rf", args.output + ".fusion.bedpe"])
subprocess.call(["rm", "-rf", args.output + ".fusion_comp.bedpe"])
def comp_main(args):
if os.path.getsize(args.fusion1) == 0:
hOUT = open(args.output, 'w')
hOUT.close()
return
if args.type1 in [
"fusionfusion", "fusionfusion_part", "star_fusion",
"genomon_fusion", "mapsplice2", "tophat_fusion"
] and args.type2 == "genomonSV":
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe",
args.sv_margin_major, args.sv_margin_minor,
args.type1)
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe",
args.margin, args.margin, "genomonSV")
elif args.type2 in [
"fusionfusion", "fusionfusion_part", "star_fusion",
"genomon_fusion", "mapsplice2", "tophat_fusion"
] and args.type1 == "genomonSV":
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe",
args.margin, args.margin, "genomonSV")
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe",
args.sv_margin_major, args.sv_margin_minor,
args.type2)
else:
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe",
args.margin, args.margin, args.type1)
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe",
args.margin, args.margin, args.type2)
hOUT = open(args.output + ".fusion_comp.bedpe", 'w')
subprocess.check_call([
"bedtools", "pairtopair", "-a", args.output + ".fusion1.bedpe", "-b",
args.output + ".fusion2.bedpe"
],
stdout=hOUT)
hOUT.close()
# create dictionary
fusion_comp = {}
hIN = open(args.output + ".fusion_comp.bedpe", 'r')
for line in hIN:
F = line.rstrip('\n').split('\t')
fusion_comp[F[6]] = F[16]
hIN.close()
# add SV annotation to fusion
hIN = open(args.fusion1, 'r')
hOUT = open(args.output, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
chr1, pos1, dir1, chr2, pos2, dir2 = process.get_position(
F, args.type1)
ID = chr1 + ':' + dir1 + pos1 + '-' + chr2 + ':' + dir2 + pos2
SV_info = fusion_comp[ID] if ID in fusion_comp else "---"
print >> hOUT, '\t'.join(F) + '\t' + SV_info
hIN.close()
hOUT.close()
# remove intermediate files
subprocess.check_call(["rm", "-rf", args.output + ".fusion1.bedpe"])
subprocess.check_call(["rm", "-rf", args.output + ".fusion2.bedpe"])
subprocess.check_call(["rm", "-rf", args.output + ".fusion_comp.bedpe"])
def comp_main(args):
if os.path.getsize(args.fusion1) == 0:
hOUT = open(args.output, 'w')
hOUT.close()
return
if args.type1 in ["fusionfusion", "fusionfusion_part", "star_fusion", "genomon_fusion", "mapsplice2", "tophat_fusion"] and args.type2 == "genomonSV":
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe", 500000, 10, args.type1)
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe", 10, 10, "genomonSV")
elif args.type2 in ["fusionfusion", "fusionfusion_part", "star_fusion", "genomon_fusion", "mapsplice2", "tophat_fusion"] and args.type1 == "genomonSV":
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe", 10, 10, "genomonSV")
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe", 500000, 10, args.type2)
else:
process.convert_to_bedpe(args.fusion1, args.output + ".fusion1.bedpe", 10, 10, args.type1)
process.convert_to_bedpe(args.fusion2, args.output + ".fusion2.bedpe", 10, 10, args.type2)
hOUT = open(args.output + ".fusion_comp.bedpe", 'w')
subprocess.call([args.bedtools_path + "/bedtools", "pairtopair", "-a", args.output + ".fusion1.bedpe", "-b", args.output + ".fusion2.bedpe"], stdout = hOUT)
hOUT.close()
# create dictionary
fusion_comp = {}
hIN = open(args.output + ".fusion_comp.bedpe", 'r')
for line in hIN:
F = line.rstrip('\n').split('\t')
fusion_comp[F[6]] = F[16]
hIN.close()
# add SV annotation to fusion
hIN = open(args.fusion1, 'r')
hOUT = open(args.output, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
chr1, pos1, dir1, chr2, pos2, dir2 = process.get_position(F, args.type1)
ID = chr1 + ':' + dir1 + pos1 + '-' + chr2 + ':' + dir2 + pos2
SV_info = fusion_comp[ID] if ID in fusion_comp else "---"
print >> hOUT, '\t'.join(F) + '\t' + SV_info
hIN.close()
hOUT.close()
# remove intermediate files
subprocess.call(["rm", "-rf", args.output + ".fusion1.bedpe"])
subprocess.call(["rm", "-rf", args.output + ".fusion2.bedpe"])
subprocess.call(["rm", "-rf", args.output + ".fusion_comp.bedpe"])
