def filt_main(args):
annotation_dir = args.db_dir
ref_gene_bed = annotation_dir + "/refGene.bed.gz"
ref_exon_bed = annotation_dir + "/refExon.bed.gz"
ens_gene_bed = annotation_dir + "/ensGene.bed.gz"
ens_exon_bed = annotation_dir + "/ensExon.bed.gz"
grch2ucsc_file = annotation_dir + "/grch2ucsc.txt"
ref_gene_tb = pysam.TabixFile(ref_gene_bed)
ref_exon_tb = pysam.TabixFile(ref_exon_bed)
ens_gene_tb = pysam.TabixFile(ens_gene_bed)
ens_exon_tb = pysam.TabixFile(ens_exon_bed)
# relationship between CRCh and UCSC chromosome names
grch2ucsc = {}
with open(grch2ucsc_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
grch2ucsc[F[0]] = F[1]
hIN = open(args.fusion, '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.type)
read_num = process.get_read_num(F, args.type)
if read_num < args.thres: continue
if chr1 in ["MT", "chrM", "hs37d5"] or chr2 in ["MT", "chrM", "hs37d5"]: continue
if chr1.startswith("GL0") or chr2.startswith("GL0"): continue
chr1_ucsc = grch2ucsc[chr1] if chr1 in grch2ucsc else chr1
chr2_ucsc = grch2ucsc[chr2] if chr2 in grch2ucsc else chr2
gene1 = annotation.get_gene_info(chr1_ucsc, pos1, ref_gene_tb, ens_gene_tb)
gene2 = annotation.get_gene_info(chr2_ucsc, pos2, ref_gene_tb, ens_gene_tb)
junction1 = annotation.get_junc_info(chr1_ucsc, pos1, ref_exon_tb, ens_exon_tb, 5)
junction2 = annotation.get_junc_info(chr2_ucsc, pos2, ref_exon_tb, ens_exon_tb, 5)
same_gene_flag = 0
for g1 in gene1:
for g2 in gene2:
if g1 == g2: same_gene_flag = 1
if args.filter_same_gene and same_gene_flag == 1: continue
junc_test = 0
if (';'.join(junction1).find("start") != -1 and ';'.join(junction2).find("end") != -1) or (';'.join(junction1).find("end") != -1 and ';'.join(junction2).find("start") != -1):
junc_test = 1
if args.filter_unspliced and junc_test == 0: continue
print >> hOUT, '\t'.join(F)
hIN.close()
hOUT.close()
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 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"])
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 filt_main(args):
"""
annotation_dir = args.db_dir
ref_gene_bed = annotation_dir + "/refGene.bed.gz"
ref_exon_bed = annotation_dir + "/refExon.bed.gz"
ens_gene_bed = annotation_dir + "/ensGene.bed.gz"
ens_exon_bed = annotation_dir + "/ensExon.bed.gz"
grch2ucsc_file = annotation_dir + "/grch2ucsc.txt"
ref_gene_tb = pysam.TabixFile(ref_gene_bed)
ref_exon_tb = pysam.TabixFile(ref_exon_bed)
ens_gene_tb = pysam.TabixFile(ens_gene_bed)
ens_exon_tb = pysam.TabixFile(ens_exon_bed)
# relationship between CRCh and UCSC chromosome names
grch2ucsc = {}
with open(grch2ucsc_file, 'r') as hin:
for line in hin:
F = line.rstrip('\n').split('\t')
grch2ucsc[F[0]] = F[1]
"""
annot_utils.gene.make_gene_info(args.output + ".tmp.refGene.bed.gz",
"refseq", args.genome_id, args.grc, False)
annot_utils.gene.make_gene_info(args.output + ".tmp.ensGene.bed.gz",
"gencode", args.genome_id, args.grc, False)
annot_utils.exon.make_exon_info(args.output + ".tmp.refExon.bed.gz",
"refseq", args.genome_id, args.grc, False)
annot_utils.exon.make_exon_info(args.output + ".tmp.ensExon.bed.gz",
"gencode", args.genome_id, args.grc, False)
ref_gene_tb = pysam.TabixFile(args.output + ".tmp.refGene.bed.gz")
ens_gene_tb = pysam.TabixFile(args.output + ".tmp.ensGene.bed.gz")
ref_exon_tb = pysam.TabixFile(args.output + ".tmp.refExon.bed.gz")
ens_exon_tb = pysam.TabixFile(args.output + ".tmp.ensExon.bed.gz")
hIN = open(args.fusion, '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.type)
read_num = process.get_read_num(F, args.type)
if read_num < args.thres: continue
if chr1 in ["MT", "chrM", "hs37d5"
] or chr2 in ["MT", "chrM", "hs37d5"]:
continue
if chr1.startswith("GL0") or chr2.startswith("GL0"): continue
# chr1_ucsc = grch2ucsc[chr1] if chr1 in grch2ucsc else chr1
# chr2_ucsc = grch2ucsc[chr2] if chr2 in grch2ucsc else chr2
gene1 = annotation.get_gene_info(chr1, pos1, ref_gene_tb, ens_gene_tb)
gene2 = annotation.get_gene_info(chr2, pos2, ref_gene_tb, ens_gene_tb)
junction1 = annotation.get_junc_info(chr1, pos1, ref_exon_tb,
ens_exon_tb, 5)
junction2 = annotation.get_junc_info(chr2, pos2, ref_exon_tb,
ens_exon_tb, 5)
same_gene_flag = 0
for g1 in gene1:
for g2 in gene2:
if g1 == g2: same_gene_flag = 1
if args.filter_same_gene and same_gene_flag == 1: continue
junc_test = 0
if (';'.join(junction1).find("start") != -1
and ';'.join(junction2).find("end") != -1) or (
';'.join(junction1).find("end") != -1
and ';'.join(junction2).find("start") != -1):
junc_test = 1
if args.filter_unspliced and junc_test == 0: continue
print >> hOUT, '\t'.join(F)
hIN.close()
hOUT.close()
subprocess.check_call(["rm", "-rf", args.output + ".tmp.refGene.bed.gz"])
subprocess.check_call(["rm", "-rf", args.output + ".tmp.ensGene.bed.gz"])
subprocess.check_call(["rm", "-rf", args.output + ".tmp.refExon.bed.gz"])
subprocess.check_call(["rm", "-rf", args.output + ".tmp.ensExon.bed.gz"])
subprocess.check_call(
["rm", "-rf", args.output + ".tmp.refGene.bed.gz.tbi"])
subprocess.check_call(
["rm", "-rf", args.output + ".tmp.ensGene.bed.gz.tbi"])
subprocess.check_call(
["rm", "-rf", args.output + ".tmp.refExon.bed.gz.tbi"])
subprocess.check_call(
["rm", "-rf", args.output + ".tmp.ensExon.bed.gz.tbi"])
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"])