Mercurial > repos > artbio > lumpy_smoove
changeset 6:ad8853ee9909 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
| author | artbio |
|---|---|
| date | Sun, 14 Feb 2021 23:59:42 +0000 |
| parents | bd4135caa3fa |
| children | 8b0005fdfd04 |
| files | lumpy_smoove.xml test-data/test_vcf2hrdetect.tab test-data/test_vcf2hrdetect.vcf vcf2hrdetect.py vcf2hrdetect.xml |
| diffstat | 5 files changed, 666 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/lumpy_smoove.xml Fri Sep 25 10:43:20 2020 +0000 +++ b/lumpy_smoove.xml Sun Feb 14 23:59:42 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy5"> +<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy6"> <description>find structural variants using the smoove workflow</description> <macros> <import>macro_lumpy_smoove.xml</import> @@ -102,7 +102,7 @@ <param name="choices" value="yes"/> <param name="bedmask" value="exclude.bed"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="12"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -112,7 +112,7 @@ <param name="choices" value="yes"/> <param name="bedmask" value="exclude.bed"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="12"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -121,7 +121,7 @@ <param name="tumor_bam" value="celegans_RG_2.bam"/> <param name="choices" value="no"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="12"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -130,7 +130,7 @@ <param name="tumor_bam" value="celegans_RG_1.bam"/> <param name="choices" value="no"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="12"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -139,7 +139,7 @@ <param name="tumor_bam" value="celegans_RG_2.bam"/> <param name="choices" value="no"/> <param name="prpos" value="yes"/> - <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="12"/> </test> <test> <param name="reference_source_selector" value="history" /> @@ -148,7 +148,7 @@ <param name="single_bam" value="celegans_RG_1.bam"/> <param name="choices" value="no"/> <param name="prpos" value="no"/> - <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/> + <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="12"/> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf2hrdetect.tab Sun Feb 14 23:59:42 2021 +0000 @@ -0,0 +1,180 @@ +chr1 pos1 chr2 pos2 type +1 28515659 19 24027918 TRA +1 42552553 4 44842163 TRA +1 44059282 1 44059890 INV +1 64897140 6 159204434 TRA +1 66804423 13 59377693 TRA +1 80794627 1 80795137 INV +1 91151631 8 85437297 TRA +1 105428633 7 93357413 TRA +1 119401195 15 51189306 TRA +1 168024578 19 24033135 TRA +1 221827800 13 61315891 TRA +1 234805693 16 59323740 TRA +2 12019022 7 52399206 TRA +2 77358259 18 59713754 TRA +2 78091959 4 174044216 TRA +2 153997618 17 74377266 TRA +2 160095376 2 160095824 INV +2 178351450 19 52567370 TRA +2 178351470 19 52567638 TRA +2 204273805 4 68944782 TRA +3 12818457 5 144122990 TRA +3 38399708 8 75876952 TRA +3 48372309 7 32225987 TRA +3 54428366 12 28226427 TRA +3 75960769 11 130675918 TRA +3 105828859 5 141379626 TRA +3 151748833 3 176444683 INV +3 158034493 6 32688592 TRA +3 182298978 11 94948981 TRA +3 182299013 9 1940734 TRA +3 184156702 20 231409 TRA +3 192376521 10 65545580 TRA +4 81136688 6 68923562 TRA +4 99513602 6 32589570 TRA +4 162642267 X 3599701 TRA +4 162642407 X 3599706 TRA +4 175534267 10 123120353 TRA +4 183256660 8 131547788 TRA +4 186382139 9 129005120 TRA +5 5595231 15 52589534 TRA +5 37709852 7 8663298 TRA +5 53122606 5 53125511 INV +5 53122773 5 53125484 INV +5 54865791 10 75489275 TRA +5 54865801 10 75489000 TRA +5 147553039 5 147554616 INV +5 157223490 5 176652060 INV +5 157223548 11 3760878 TRA +5 169597700 5 169598748 INV +5 176651964 11 3760899 TRA +6 17608998 X 117432517 TRA +6 26625483 7 68758443 TRA +6 37295025 12 22085955 TRA +6 74156485 14 71480241 TRA +6 107307808 8 105231718 TRA +6 161336425 7 85956546 TRA +7 70420972 7 70438890 INV +7 98015910 X 136092975 TRA +7 111053752 12 108203254 TRA +7 127930431 16 76865795 TRA +7 156387047 7 156387226 INV +8 30145409 17 7167951 TRA +8 59616000 16 3354097 TRA +8 96265720 19 18835613 TRA +8 140475500 12 58359059 TRA +8 140475502 11 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_vcf2hrdetect.vcf Sun Feb 14 23:59:42 2021 +0000 @@ -0,0 +1,403 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##fileDate=20201029 +##reference=reference.fa +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants"> +##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants"> +##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples"> +##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples"> +##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples"> +##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples"> +##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=INV,Description="Inversion"> +##ALT=<ID=DUP:TANDEM,Description="Tandem duplication"> +##ALT=<ID=INS,Description="Insertion of novel sequence"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant"> +##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant"> +##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant"> +##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations"> +##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally"> +##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)"> +##contig=<ID=1,length=249250621> +##contig=<ID=2,length=243199373> +##contig=<ID=3,length=198022430> +##contig=<ID=4,length=191154276> +##contig=<ID=5,length=180915260> +##contig=<ID=6,length=171115067> 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+##contig=<ID=GL000227.1,length=128374> +##contig=<ID=GL000228.1,length=129120> +##contig=<ID=GL000214.1,length=137718> +##contig=<ID=GL000221.1,length=155397> +##contig=<ID=GL000209.1,length=159169> +##contig=<ID=GL000218.1,length=161147> +##contig=<ID=GL000220.1,length=161802> +##contig=<ID=GL000213.1,length=164239> +##contig=<ID=GL000211.1,length=166566> +##contig=<ID=GL000199.1,length=169874> +##contig=<ID=GL000217.1,length=172149> +##contig=<ID=GL000216.1,length=172294> +##contig=<ID=GL000215.1,length=172545> +##contig=<ID=GL000205.1,length=174588> +##contig=<ID=GL000219.1,length=179198> +##contig=<ID=GL000224.1,length=179693> +##contig=<ID=GL000223.1,length=180455> +##contig=<ID=GL000195.1,length=182896> +##contig=<ID=GL000212.1,length=186858> +##contig=<ID=GL000222.1,length=186861> +##contig=<ID=GL000200.1,length=187035> +##contig=<ID=GL000193.1,length=189789> +##contig=<ID=GL000194.1,length=191469> +##contig=<ID=GL000225.1,length=211173> +##contig=<ID=GL000192.1,length=547496> +##smoove_version=0.2.5 +##smoove_count_stats=TARGET-21-PAMXZY-15A-01D:0,646270,0,297568 +##smoove_count_stats=TARGET-21-PAMXZY-09A-03D:0,504761,0,141470 +##source=LUMPY +##bcftools_annotateVersion=1.10.2+htslib-1.10.2 +##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Thu Oct 29 18:30:42 2020 +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Thu Oct 29 18:30:42 2020 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TARGET-21-PAMXZY-15A-01D TARGET-21-PAMXZY-09A-03D +1 14436660 4 N <DUP> 40.38 . SVTYPE=DUP;SVLEN=1903;END=14438563;STRANDS=-+:11;IMPRECISE;CIPOS=-219,29;CIEND=-30,224;CIPOS95=-93,4;CIEND95=-4,95;SU=11;PE=11;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:19:0.05:-0,-2,-4:21:21:0:21:0:21:0:0:0:0:0 0/1:40:40.33:-7,-3,-8:110:98:11:97:10:44:0:0:53:10:0.093 +1 28515659 1971_1 N N]19:24027918] 194.49 . SVTYPE=BND;STRANDS=++:12;IMPRECISE;CIPOS=-24,212;CIEND=-30,228;CIPOS95=-4,93;CIEND95=-4,73;MATEID=1971_2;EVENT=1971;SU=12;PE=12;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:162:0:-0,-16,-54:56:55:0:54:0:23:0:0:31:0:0 0/1:194:194.49:-27,-8,-47:76:61:14:61:14:0:0:0:61:14:0.19 +1 42552553 1942_1 N N[4:44842163[ 59.54 . SVTYPE=BND;STRANDS=+-:7;IMPRECISE;CIPOS=-15,285;CIEND=-238,29;CIPOS95=-1,137;CIEND95=-86,5;MATEID=1942_2;EVENT=1942;SU=7;PE=7;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:57:0:-3,-9,-34:40:37:2:37:2:0:0:0:37:2:0.051 0/1:59:59.54:-16,-10,-51:71:61:9:61:9:0:0:0:61:9:0.13 +1 43694066 15 N <DEL> 353.17 . SVTYPE=DEL;SVLEN=-1472;END=43695538;STRANDS=+-:26;IMPRECISE;CIPOS=-30,203;CIEND=-202,29;CIPOS95=-7,39;CIEND95=-55,4;SU=26;PE=26;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:60:0:-5,-11,-43:52:48:4:47:3:23:0:1:24:2:0.06 0/1:200:353.17:-47,-11,-74:124:99:24:98:24:47:0:2:51:22:0.2 +1 44059282 17_1 N N]1:44059890] 50.66 . SVTYPE=BND;STRANDS=++:11;IMPRECISE;CIPOS=-30,193;CIEND=-30,225;CIPOS95=-7,65;CIEND95=-4,94;MATEID=17_2;EVENT=17;SU=11;PE=11;SR=0;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:36:0:-3,-7,-27:33:30:2:30:2:0:0:0:30:2:0.062 0/1:50:50.65:-13,-8,-38:54:46:7:46:7:0:0:0:46:7:0.13 +1 44059890 17_2 N N]1:44059282] 50.66 . 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2hrdetect.py Sun Feb 14 23:59:42 2021 +0000 @@ -0,0 +1,41 @@ +import sys + +handle = open(sys.argv[1], 'r') +vcfdict = dict() +tabdict = dict() +for line in handle: + if line[0] == "#": + continue + else: + tabline = line[:-1].split("\t") + vcfdict[tabline[2]] = tabline +for id in vcfdict.keys(): + if "_1" in id: + newid = id[:-2] + pointbreak = vcfdict[id][4] + if "]" in pointbreak: + coordbreak = pointbreak.split("]")[1].split(":")[1] + chrom = pointbreak.split("]")[1].split(":")[0] + elif "[" in pointbreak: + coordbreak = pointbreak.split("[")[1].split(":")[1] + chrom = pointbreak.split("[")[1].split(":")[0] + if vcfdict[id][0] == chrom: + tabdict[newid] = [chrom, vcfdict[id][1], chrom, coordbreak, "INV"] + else: + tabdict[newid] = [vcfdict[id][0], vcfdict[id][1], + chrom, coordbreak, "TRA"] +for id in list(vcfdict): + if "_" in id: + del(vcfdict[id]) +for id in vcfdict.keys(): # only sv that are not of type TRA or INV + chr1 = vcfdict[id][0] + chr2 = vcfdict[id][0] + pos1 = vcfdict[id][1] + pos2 = vcfdict[id][7].split("END=")[1].split(";")[0] + type = vcfdict[id][7].split("SVTYPE=")[1].split(";")[0] + tabdict[id] = [chr1, pos1, chr2, pos2, type] +out = open(sys.argv[2], 'w') +out.write("chr1\tpos1\tchr2\tpos2\ttype\n") +for key in tabdict: + line = "\t".join(tabdict[key]) + "\n" + out.write(line)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2hrdetect.xml Sun Feb 14 23:59:42 2021 +0000 @@ -0,0 +1,35 @@ +<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> + <description>to tabular hrdetect</description> + <macros> + <import>macro_lumpy_smoove.xml</import> + </macros> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + @pipefail@ + python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular' + ]]></command> + <inputs> + <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/> + </inputs> + + <outputs> + <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" /> + </outputs> + + <tests> + <test> + <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> + <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> + </test> + </tests> + <help> +**vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with +the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv) + </help> + + <citations> + <citation type="doi">10.1038/nm.4292</citation> + </citations> +</tool>