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vrohnievrohnie
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switched clove latest build from git code
1 parent 4c2c20b commit 85202b2

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5 files changed

+188
-31
lines changed

5 files changed

+188
-31
lines changed

‎clove/Dockerfile

+2-1
Original file line numberDiff line numberDiff line change
@@ -13,4 +13,5 @@ RUN apt-get -y install default-jre
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WORKDIR /bin
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#RUN wget https://github.com/PapenfussLab/clove/releases/download/v0.17/clove-0.17-jar-with-dependencies.jar
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RUN wget https://github.com/PapenfussLab/clove/releases/download/v0.15/clove-0.15-jar-with-dependencies.jar
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#RUN wget https://github.com/PapenfussLab/clove/releases/download/v0.15/clove-0.15-jar-with-dependencies.jar
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ADD clove.jar /bin

‎clove/clove.jar

2.49 MB
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‎clove/clove.sh

+2-1
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,8 @@ GRIDSS_VCF="${outdir/clove/gridss}/svs.vcf"
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GRIDSS_Filtered_VCF="${outdir/clove/gridss}/svs_filtered.vcf"
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DELLY_VCF="${outdir/clove/delly_0.7.9}/delly_0.7.9.vcf"
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CLOVE="/bin/clove-0.15-jar-with-dependencies.jar"
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#CLOVE="/bin/clove-0.15-jar-with-dependencies.jar"
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CLOVE="/bin/clove.jar"
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#if [ -s "$GRIDSS_VCF" ] && [ -s "$DELLY_VCF" ]; then
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if [ -s "$GRIDSS_VCF" ]; then

‎sv_sim/HackBedToComplexVCF.py

+153
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,153 @@
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from bed_maker_supplementary import *
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import sys
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import argparse
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import csv
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from Bio import SeqIO
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# adapted from : https://github.com/PapenfussLab/sv_benchmark/blob/master/breakdancer2vcf.py
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(
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prog='HockBedToVCF', description='Reformat the bedmaker output to VCF')
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parser.add_argument('-i', '--inFile', type=str, nargs='+',
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help='file containing summary bed file')
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parser.add_argument('-r', '--reference', type=str, nargs='+',
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help='base reference fasta')
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parser.add_argument('-p', '--hasPlasmid', type=bool, nargs='?',
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const=True, default=False,
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help='indicate if ref has plasmids')
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# parser.add_argument('-c', '--contigs', type=str, nargs='+',
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# help='contigs and legths of contigs in form id:length')
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args = parser.parse_args()
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in_file = vars(args).get("inFile")[0]
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reference = vars(args).get("reference")[0]
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has_plasmids = vars(args).get("hasPlasmid")
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plasmid_length = 0
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print(args)
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if in_file is None or reference is None:
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parser.print_help()
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sys.exit(1)
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import os
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vcf_path = in_file.replace(".bed","-complex.vcf")
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vcf_file = open(vcf_path, "w")
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vcf_file.write("##fileformat=VCFv4.2\n")
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vcf_file.write("##ALT=<ID=DEL,Description=\"Deletion\">\n")
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vcf_file.write("##ALT=<ID=DUP,Description=\"Duplication\">\n")
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vcf_file.write("##ALT=<ID=INV,Description=\"Inversion\">\n")
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vcf_file.write("##ALT=<ID=BND,Description=\"Translocation\">\n")
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vcf_file.write("##ALT=<ID=INS,Description=\"Insertion\">\n")
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vcf_file.write("##FILTER=<ID=PASS,Description=\"All filters passed\">\n")
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vcf_file.write("##INFO=<ID=CHR2,Number=1,Type=String,Description=\"Chromosome for POS2 coordinate in case of an inter-chromosomal translocation\">\n")
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vcf_file.write("##INFO=<ID=POS2,Number=1,Type=Integer,Description=\"Genomic position for CHR2 in case of an inter-chromosomal translocation\">\n")
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vcf_file.write("##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the structural variant\">\n")
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vcf_file.write("##INFO=<ID=SVTYPE,Number=1,Type=String,Description=\"BE for breakend and BND for breakpoint \">\n")
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vcf_file.write("##INFO=<ID=SV_DEF,Number=1,Type=String,Description=\"Definition of complex SV \">\n")
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vcf_file.write("##INFO=<ID=SVLEN,Number=1,Type=Integer,Description=\"Length of SV \">\n")
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vcf_file.write("##INFO=<ID=EVENT,Number=1,Type=String,Description=\"EVENT the SV belongs to \">\n")
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vcf_file.write("##INFO=<ID=MATEID,Number=1,Type=String,Description=\"ID of mate breakend or breakpoint \">\n")
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vcf_file.write("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n")
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vcf_file.write(f"##reference={vars(args).get('reference')[0]}\n")
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# for cont in vars(args).get("contigs"):
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# conts = cont.split(":")
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# vcf_file.write(f"##contig=<ID={conts[0]},length={conts[1]}>\n")
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referenceFile = open(reference, 'r')
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for rec in SeqIO.parse(referenceFile, 'fasta'):
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name = rec.id
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seq = rec.seq
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seqLen = len(rec)
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vcf_file.write(f"##contig=<ID={name},length={seqLen}>\n")
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if has_plasmids and name == "plasmid":
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plasmid_length = seqLen
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print(plasmid_length)
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vcf_file.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tCHR1\n")
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def toVcfBreakend(localChr, localPos, localPositive, remoteChr, remotePos, remotePositive):
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if remotePositive:
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remote = "]" + remoteChr + ":" + str(remotePos) + "]"
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else:
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remote = "[" + remoteChr + ":" + str(remotePos) + "["
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if localPositive:
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return "N" + remote
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else:
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return remote + "N"
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with open(in_file) as file:
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bed = csv.reader(file, delimiter="\t")
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for idx, line in enumerate(bed):
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chr1 = line[0]
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start = int(line[1])
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end = int(line[2])
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sv_def = line[3]
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insertion = line[4]
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if sv_def == options_dict.get("del"):
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vcf_file.write(f"{chr1}\t{start}\tDEL_{str(idx)}\tN\t<DEL>\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=DEL;SV_DEF={sv_def};EVENT=DEL_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("ins"):
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if has_plasmids:
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vcf_file.write(f"{chr1}\t{start}\tINS_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,'plasmid',0,False)}\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=BND;SV_DEF={sv_def};EVENT=INS_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end}\tINS_{str(idx)}b\tN\t{toVcfBreakend(chr1,end,False,'plasmid',plasmid_length,True)}\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=BND;SV_DEF={sv_def};EVENT=INS_{str(idx)}\tGT\t1/1\n")
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else:
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vcf_file.write(f"{chr1}\t{start}\tINS_{str(idx)}\tN\t<INS>\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=INS;SV_DEF={sv_def};EVENT=INS_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("inv"):
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vcf_file.write(f"{chr1}\t{start}\tINV_{str(idx)}\tN\t<INV>\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=INV;SV_DEF={sv_def};EVENT=INV_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("tdu"):
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vcf_file.write(f"{chr1}\t{start}\tTDU_{str(idx)}\tN\t<DUP>\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=DUP;SV_DEF={sv_def};EVENT=TDU_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("itd"):
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vcf_file.write(f"{chr1}\t{start}\tITD_{str(idx)}b\tN\t<DUP>\t.\tPASS\tCHR2={chr1};END={end};SVLEN={str(end-start)};SVTYPE=BND;SV_DEF={sv_def};EVENT=ITD_{str(idx)}\tGT\t1/1\n")
113+
elif sv_def in (options_dict.get("tcp"), options_dict.get("txp"), options_dict.get("tci"), options_dict.get("txi"), options_dict.get("chr")):
114+
inserts = insertion.split(":")
115+
chr2 = inserts[1]
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pos2 = int(inserts[2])
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direction = inserts[3]
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if sv_def in {options_dict.get("tcp"), options_dict.get("tci")}:
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vcf_file.write(f"{chr2}\t{pos2}\tTCP_{str(idx)}a\tN\t<DUP>\t.\tPASS\tCHR2={chr2};END={pos2+1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TCP_{str(idx)}\tGT\t1/1\n")
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elif sv_def in {options_dict.get("txp"), options_dict.get("txi")}:
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vcf_file.write(f"{chr2}\t{pos2}\tTCP_{str(idx)}a\tN\t<TRA>\t.\tPASS\tCHR2={chr2};END={pos2+1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TCP_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("chr"):
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if direction == "forward":
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vcf_file.write(f"{chr1}\t{start}\tCHR_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,chr2,pos2+1,False)}\t.\tPASS\tCHR2={chr2};END={pos2+1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=CHR_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end+1}\tCHR_{str(idx)}b\tN\t{toVcfBreakend(chr1,end+1,False,chr2,pos2,True)}\t.\tPASS\tCHR2={chr2};END={pos2};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=CHR_{str(idx)}\tGT\t1/1\n")
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else:
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vcf_file.write(f"{chr1}\t{start}\tCHR_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,chr2,pos2,True)}\t.\tPASS\tCHR2={chr2};END={pos2};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=CHR_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end+1}\tCHR_{str(idx)}b\tN\t{toVcfBreakend(chr1,end+1,False,chr2,pos2+1,False)}\t.\tPASS\tCHR2={chr2};END={pos2+1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=CHR_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("sub"):
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if has_plasmids:
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vcf_file.write(f"{chr1}\t{start}\tSUB_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,'plasmid',0,False)}\t.\tPASS\tCHR2={chr1};END={start};SVLEN=0;SVTYPE=BE;SV_DEF={sv_def};EVENT=SUB_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end}\tSUB_{str(idx)}b\tN\t{toVcfBreakend(chr1,start,False,'plasmid',plasmid_length,True)}\t.\tPASS\tCHR2={chr1};END={end};SVLEN=0;SVTYPE=BE;SV_DEF={sv_def};EVENT=SUB_{str(idx)}\tGT\t1/1\n")
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else:
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vcf_file.write(f"{chr1}\t{start}\tSUB_{str(idx)}a\tN\tN]{chr1}:{start}]\t.\tPASS\tCHR2={chr1};END={start};SVLEN=0;SVTYPE=BE;SV_DEF={sv_def};EVENT=SUB_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end}\tSUB_{str(idx)}b\tN\t[{chr1}:{end}[N\t.\tPASS\tCHR2={chr1};END={end};SVLEN=0;SVTYPE=BE;SV_DEF={sv_def};EVENT=SUB_{str(idx)}\tGT\t1/1\n")
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elif sv_def == options_dict.get("tcs"):
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inserts = insertion.split(":")
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chr2 = inserts[1]
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pos1 = int(inserts[0])
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pos2 = int(inserts[2])
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direction = inserts[3]
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if direction == "forward":
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vcf_file.write(f"{chr1}\t{start}\tTCS_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,chr2,pos1,False)}\t.\tPASS\tCHR2={chr2};END={pos1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TCS_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end}\tTCS_{str(idx)}b\tN\t{toVcfBreakend(chr1,end,False,chr2,pos2+1,True)}\t.\tPASS\tCHR2={chr2};END={pos2+1};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TCS_{str(idx)}\tGT\t1/1\n")
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else:
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vcf_file.write(f"{chr1}\t{start}\tTCS_{str(idx)}a\tN\t{toVcfBreakend(chr1,start,True,chr2,pos2+1,True)}\t.\tPASS\tCHR2={chr2};END={end};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TSI_{str(idx)}\tGT\t1/1\n")
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vcf_file.write(f"{chr1}\t{end}\tTCS_{str(idx)}b\tN\t{toVcfBreakend(chr1,end,False,chr2,pos1,False)}\t.\tPASS\tCHR2={chr2};END={end};SVLEN=0;SVTYPE=BND;SV_DEF={sv_def};EVENT=TSI_{str(idx)}\tGT\t1/1\n")
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else:
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print("UNHANDLED VARIANT CALL: " + sv_def + " " + options_dict.get("tci"))
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vcf_file.close()

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