| Previous changeset 2:4934c0ac6197 (2022-03-17) Next changeset 4:9793bc5d741b (2024-06-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17 |
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modified:
tbvcfreport.xml test-data/rif_resistant.results.json test-data/rif_resistant.vcf test-data/rif_resistant_drug_resistance_report.html test-data/rif_resistant_drug_resistance_report.txt test-data/rif_resistant_variants_report.html test-data/rif_resistant_variants_report.txt test-data/rif_resistant_variants_report_with_lineage.html test-data/rif_resistant_variants_report_with_lineage.txt test-data/vcf_with_no_protein_report.html test-data/vcf_with_no_protein_report.txt |
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| diff -r 4934c0ac6197 -r 42818629ec4c tbvcfreport.xml --- a/tbvcfreport.xml Thu Mar 17 07:33:00 2022 +0000 +++ b/tbvcfreport.xml Fri May 31 20:06:49 2024 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0"> +<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="AGPL-3.0-or-later"> <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description> <macros> - <token name="@TOOL_VERSION@">0.1.10</token> + <token name="@TOOL_VERSION@">1.0.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement> @@ -62,7 +62,7 @@ <inputs> <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" /> <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" /> - <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" /> + <param argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" /> <section name="adv" title="Advanced options" expanded="false"> <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify COMBAT-TB-NeoDB URI" help="For people with their own deployment of COMBAT-TB-NeoDB" /> </section> @@ -102,7 +102,7 @@ <![CDATA[ **tbvcfreport - @TOOL_VERSION@** - **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB (https://neodb.sanbi.ac.za) + **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/). **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report. |
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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant.results.json --- a/test-data/rif_resistant.results.json Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant.results.json Fri May 31 20:06:49 2024 +0000 |
| [ |
| b'@@ -1,1 +1,704 @@\n-{"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], ["Chromosome", 763409], ["Chromosome", 763410], ["Chromosome", 763411], ["Chromosome", 763412], ["Chromosome", 763413], ["Chromosome", 763414], ["Chromosome", 763415], ["Chromosome", 763416], ["Chromosome", 763417], ["Chromosome", 763418], ["Chromosome", 763419], ["Chromosome", 763420], ["Chromosome", 1834082], ["Chromosome", 1834083], ["Chromosome", 1834084], ["Chromosome", 1834085], ["Chromosome", 1834086], ["Chromosome", 1834087], ["Chromosome", 1834088], ["Chromosome", 1834089], ["Chromosome", 1834090], ["Chromosome", 1834091], ["Chromosome", 1834092], ["Chromosome", 1834093], ["Chromosome", 1834094], ["Chromosome", 1834095], ["Chromosome", 1834251], ["Chromosome", 1834252], ["Chromosome", 1834253], ["Chromosome", 1834254], ["Chromosome", 1834255], ["Chromosome", 1834256], ["Chromosome", 1834257], ["Chromosome", 1834258], ["Chromosome", 1834259], ["Chromosome", 1834260], ["Chromosome", 1834261], ["Chromosome", 1834262], ["Chromosome", 1834263], ["Chromosome", 1834264], ["Chromosome", 1834265], ["Chromosome", 1834266], ["Chromosome", 1834267], ["Chromosome", 1834268], ["Chromosome", 1834269], ["Chromosome", 1834270], ["Chromosome", 1834271], ["Chromosome", 1834272], ["Chromosome", 1834273], ["Chromosome", 4245997], ["Chromosome", 4245998], ["Chromosome", 4245999], ["Chromosome", 4246000], ["Chromosome", 4246001], ["Chromosome", 4246002], ["Chromosome", 4246003], ["Chromosome", 4246004], ["Chromosome", 4246005], ["Chromosome", 4246006], ["Chromosome", 4246007], ["Chromosome", 4246008], ["Chromosome", 4246009], ["Chromosome", 4246010], ["Chromosome", 4246011], ["Chromosome", 4246012], ["Chromosome", 4246155], ["Chromosome", 4246156], ["Chromosome", 4246157], ["Chromosome", 4246158], ["Chromosome", 4246159], ["Chromosome", 4246160], ["Chromosome", 4246161], ["Chromosome", 4246162], ["Chromosome", 4246163], ["Chromosome", 4246164], ["Chromosome", 4246165], ["Chromosome", 4246166], ["Chromosome", 4246167], ["Chromosome", 4246168], ["Chromosome", 4246169], ["Chromosome", 4246170], ["Chromosome", 4246171], ["Chromosome", 4246172], ["Chromosome", 4246173], ["Chromosome", 4246174], ["Chromosome", 4246175], ["Chromosome", 4246176], ["Chromosome", 4246177], ["Chromosome", 4246178], ["Chromosome", 4246179], ["Chromosome", 4246180], ["Chromosome", 4246181], ["Chromosome", 4246182], ["Chromosome", 4246183], ["Chromosome", 4246184], ["Chromosome", 4248018], ["Chromosome", 4248019], ["Chromosome", 4248020], ["Chromosome", 4248021], ["Chromosome", 4248022], ["Chromosome", 4248023], ["Chromosome", 4248024], ["Chromosome", 4248025], ["Chromosome", 4248026], ["Chromosome", 4248027], ["Chromosome", 4248028], ["Chromosome", 4248029], ["Chromosome", 4248030], ["Chromosome", 4248031], ["Chromosome", 4248032], ["Chromosome", 4248033], ["Chromosome", 4248034], ["Chromosome", 4248035], ["Chromosome", 4248036], ["Chromosome", 4248037], ["Chromosome", 4248038], ["Chromosome", 4248039], ["Chromosome", 4248040], ["Chromosome", 4248041], ["Chromosome", 4248042], ["Chromosome", 4248043], ["Chromosome", 4248044], ["Chromosome", 4248045], ["Chromosome", 4248046], ["Chromosome", 4248047], ["Chromosome", 4248184], ["Chromosome", 4248185], ["Chromosome", 4248186], ["Chromosome", 4248187], ["Chromosome", 4248188], ["Chromosome", 4248189], ["Chromosome", 4248190], ["Chromosome", 4248191], ["Chromosome", 4248192], ["Chromosome", 4248193], ["Chromosome", 4248194], ["Chromosome", 4248195], ["Chromosome", 4248196], ["Chromosome", 4248197], ["Chromosome", 4248198], ["Chromosome", 4248199], ["Chromosome", 4248200], ["Chromosome", 4248201], ["Chromosome", 4248202], ["Chromosome", 4248203], ["Chromosome", 4248204], ["Chromosome", 4248205], ["Chromosome", 4248206], ["Chromosome", 4248207], ["Chromosome", 4248208], ["Chromosome", 4248209], ["Chromosome", 4248210], ["Chromosome", 4248211], ["Chromosome", 4248212], ["Chr'..b'"percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "thyA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "ald",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "fbiD",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "Rv3083",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "whiB7",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "Rv3236c",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "lpqB",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "mtrB",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "mtrA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "fbiA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "fbiB",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "alr",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "rpoA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "ddn",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "clpC1",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "panD",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "glpK",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "embC",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "embA",\n+ "percent_depth_pass": 3.98,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "embB",\n+ "percent_depth_pass": 3.89,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "aftB",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "ubiA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "ethA",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "ethR",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "whiB6",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ },\n+ {\n+ "target": "gid",\n+ "percent_depth_pass": 0.0,\n+ "median_depth": 0.0\n+ }\n+ ],\n+ "missing_positions": [\n+ ]\n+ },\n+ "linked_samples": []\n+}\n' |
| b |
| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant.vcf --- a/test-data/rif_resistant.vcf Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant.vcf Fri May 31 20:06:49 2024 +0000 |
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| b'@@ -1,53 +1,51 @@\n ##fileformat=VCFv4.2\n ##FILTER=<ID=PASS,Description="All filters passed">\n-##bcftoolsVersion=1.9+htslib-1.9\n-##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam\n-##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa\n-##contig=<ID=MT_H37RV_BRD_V5,length=4411532>\n-##ALT=<ID=*,Description="Represents allele(s) other than observed.">\n-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n-##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n-##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n-##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n-##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n-##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n-##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n-##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n-##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##fileDate=20240531\n+##source=freeBayes v1.3.2-dirty\n+##reference=reference/ref.fa\n+##contig=<ID=Chromosome,length=4411532>\n+##phasing=none\n+##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region Chromosome:0-1495040"\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">\n+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">\n+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">\n+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">\n+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">\n-##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">\n-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">\n-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">\n-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">\n-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">\n-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">\n-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">\n-##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-rever'..b'0\n+Chromosome\t761110\t.\tA\tT\t1500.1\t.\tAB=0;AO=47;DP=48;QA=1701;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0667|GENE_Rv0667|transcript|TRANSCRIPT_Rv0667|protein_coding|1/1|c.1304A>T|p.Asp435Val|1304/3519|1304/3519|435/1172||\tGT:DP:RO:QR:AO:QA:GL\t1/1:48:0:0:47:1701:-153.05,-14.1484,0\n+Chromosome\t811753\t.\tC\tT\t1585.34\t.\tAB=0;AO=48;DP=48;QA=1796;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0715|GENE_Rv0715|transcript|TRANSCRIPT_Rv0715|protein_coding|1/1|c.12C>T|p.His4His|12/318|12/318|4/105||\tGT:DP:RO:QR:AO:QA:GL\t1/1:48:0:0:48:1796:-161.892,-14.4494,0\n+Chromosome\t1565566\t.\tC\tT\t1332.75\t.\tAB=0;AO=43;DP=43;QA=1534;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1391|GENE_Rv1391|transcript|TRANSCRIPT_Rv1391|protein_coding|1/1|c.126C>T|p.Pro42Pro|126/1257|126/1257|42/418||\tGT:DP:RO:QR:AO:QA:GL\t1/1:43:0:0:43:1534:-138.344,-12.9443,0\n+Chromosome\t1834177\t.\tA\tC\t1769.09\t.\tAB=0;AO=54;DP=54;QA=2006;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1630|GENE_Rv1630|transcript|TRANSCRIPT_Rv1630|protein_coding|1/1|c.636A>C|p.Arg212Arg|636/1446|636/1446|212/481||\tGT:DP:RO:QR:AO:QA:GL\t1/1:54:0:0:54:2006:-180.776,-16.2556,0\n+Chromosome\t1849051\t.\tC\tT\t2143.76\t.\tAB=0;AO=65;DP=65;QA=2415;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1640c|GENE_Rv1640c|transcript|TRANSCRIPT_Rv1640c|protein_coding|1/1|c.2985G>A|p.Pro995Pro|2985/3519|2985/3519|995/1172||\tGT:DP:RO:QR:AO:QA:GL\t1/1:65:0:0:65:2415:-217.563,-19.567,0\n+Chromosome\t2505085\t.\tG\tA\t1199.98\t.\tAB=0;AO=39;DP=39;QA=1425;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2231c|GENE_Rv2231c|transcript|TRANSCRIPT_Rv2231c|protein_coding|1/1|c.615C>T|p.Ala205Ala|615/1095|615/1095|205/364||\tGT:DP:RO:QR:AO:QA:GL\t1/1:39:0:0:39:1425:-128.53,-11.7402,0\n+Chromosome\t2543395\t.\tT\tC\t1871.23\t.\tAB=0;AO=58;DP=58;QA=2110;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2268c|GENE_Rv2268c|transcript|TRANSCRIPT_Rv2268c|protein_coding|1/1|c.882A>G|p.Glu294Glu|882/1470|882/1470|294/489||\tGT:DP:RO:QR:AO:QA:GL\t1/1:58:0:0:58:2110:-190.142,-17.4597,0\n+Chromosome\t2640807\t.\tG\tA\t1341.77\t.\tAB=0;AO=43;DP=43;QA=1519;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2357c|GENE_Rv2357c|transcript|TRANSCRIPT_Rv2357c|protein_coding|1/1|c.258C>T|p.Val86Val|258/1392|258/1392|86/463||\tGT:DP:RO:QR:AO:QA:GL\t1/1:43:0:0:43:1519:-136.983,-12.9443,0\n+Chromosome\t2775361\t.\tC\tT\t2221.3\t.\tAB=0;AO=69;DP=69;QA=2506;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2472|GENE_Rv2472|transcript|TRANSCRIPT_Rv2472|protein_coding|1/1|c.90C>T|p.Arg30Arg|90/294|90/294|30/97||\tGT:DP:RO:QR:AO:QA:GL\t1/1:69:0:0:69:2506:-225.745,-20.7711,0\n+Chromosome\t2789798\t.\tG\tT\t2050.68\t.\tAB=0;AO=62;DP=62;QA=2312;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2483c|GENE_Rv2483c|transcript|TRANSCRIPT_Rv2483c|protein_coding|1/1|c.1225C>A|p.Arg409Arg|1225/1743|1225/1743|409/580||\tGT:DP:RO:QR:AO:QA:GL\t1/1:62:0:0:62:2312:-208.29,-18.6639,0\n+Chromosome\t3477942\t.\tA\tG\t2414.91\t.\tAB=0;AO=75;DP=75;QA=2721;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3109|GENE_Rv3109|transcript|TRANSCRIPT_Rv3109|protein_coding|1/1|c.294A>G|p.Thr98Thr|294/1080|294/1080|98/359||\tGT:DP:RO:QR:AO:QA:GL\t1/1:75:0:0:75:2721:-245.092,-22.5773,0\n+Chromosome\t3587446\t.\tG\tA\t1562.41\t.\tAB=0;AO=49;DP=49;QA=1766;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3210c|GENE_Rv3210c|transcript|TRANSCRIPT_Rv3210c|protein_coding|1/1|c.94C>T|p.Leu32Leu|94/696|94/696|32/231||\tGT:DP:RO:QR:AO:QA:GL\t1/1:49:0:0:49:1766:-159.195,-14.7505,0\n+Chromosome\t4254431\t.\tG\tA\t1391.26\t.\tAB=0;AO=46;DP=46;QA=1617;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1518C>T|p.Asp506Asp|1518/1569|1518/1569|506/522||\tGT:DP:RO:QR:AO:QA:GL\t1/1:46:0:0:46:1617:-145.801,-13.8474,0\n+Chromosome\t4254477\t.\tT\tC\t760.909\t.\tAB=0;AO=26;DP=26;QA=933;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1472A>G|p.His491Arg|1472/1569|1472/1569|491/522||\tGT:DP:RO:QR:AO:QA:GL\t1/1:26:0:0:26:933:-84.2834,-7.82678,0\n' 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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_drug_resistance_report.html --- a/test-data/rif_resistant_drug_resistance_report.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.html Fri May 31 20:06:49 2024 +0000 |
| b |
| b'@@ -21,120 +21,167 @@\n rif_resistant Report\n </h2>\n </div>\n+ <div class="row">\n+ <table class="table table-striped table-hover table-responsive-md">\n+ <caption>Lineage Info</caption>\n+ <thead class="thead-light">\n+ <tr>\n+ <th scope="col">Lineage</th>\n+ <th scope="col">Lineage support fraction</th>\n+ <th scope="col">Family</th>\n+ <th scope="col">RD</th>\n+ </tr>\n+ </thead>\n+ <tbody>\n+ <tr>\n+ <td>lineage2</td>\n+ <td>0.9940119760479041</td>\n+ <td>East-Asian</td>\n+ <td>RD105</td>\n+ </tr>\n+ <tr>\n+ <td>lineage2.2.2</td>\n+ <td>1.0</td>\n+ <td>East-Asian (Beijing)</td>\n+ <td>RD105;RD207</td>\n+ </tr>\n+ </tbody>\n+ </table>\n+ </div>\n <hr>\n <div class="row">\n <h3 class="mb-2">\n <a class="text-body" href="https://github.com/jodyphelan/TBProfiler" target="_blank"\n- rel="noreferrer noopener">TBProfiler</a>\n+ rel="noreferrer noopener">TB-Profiler</a>\n Drug Resistance Report\n </h3>\n </div>\n <div class="row">\n- <table id="drug_resistance" class="table table-hover table-bordered table-striped table-sm" cellspacing="0">\n- <caption class="mb-3 text-info">\n- <strong>Disclaimer</strong>:\n- Drug resistance predictions are for <strong>Research Purposes Only</strong> and are produced by\n- <a class="text-info" href="https://github.com/jodyphelan/TBProfiler" target="_blank"\n- rel="noreferrer noopener">TBProfiler</a>.\n- </caption>\n- <thead class="thead-light">\n- <tr>\n- <th scope="col">Drug</th>\n- <th scope="col">Resistance</th>\n- <th scope="col">Supporting Mutations</th>\n- </tr>\n- </thead>\n- <tr>\n- <td>Isoniazid</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Rifampicin</td>\n- <td>R</td>\n- <td> <a target="_blank" href="https://explorer.sanbi.ac.za/gene?q=rpoB"\n- rel="noreferrer noopener">rpoB</a>\n- (1.0 p.Asp435Val)\n- </td>\n- </tr>\n- <tr>\n- <td>Ethambutol</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Pyrazinamide</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Streptomycin</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Ethionamide</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Fluoroquinolones</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n+ <div class="col-md-12">\n+ <p>TB-Profiler version 6.2.1 with\n+ database tbdb:82777ea (Sun Mar 17 01:14:00 2024 +0000)</p>\n+</div>\n+<div class="row">\n+ <div class="col-md-12">\n+ <table id="drug_resistance" class="table table-hover table-bordered table-striped table-responsive-md" cellspacing="0">\n+ <caption class="mb-3 text-info">\n+ <strong>Disclaimer</strong>:\n+ Drug res'..b' <td>Delaminid</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Clofazimine</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- <tr>\n- <td>Bedaquiline</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n- </tr>\n- <tr>\n- <td>Aminoglycosides</td>\n- <td>S</td>\n- <td></td>\n- </tr>\n-\n- </table>\n+ <th scope="col">Drug</th>\n+ <th scope="col">Resistance</th>\n+ <th scope="col">Supporting Mutations</th>\n+ </tr>\n+ </thead>\n+ <tr>\n+ <td>Isoniazid</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Rifampicin</td>\n+ <td>R</td>\n+ <td> <a target="_blank" href="https://explorer.sanbi.ac.za/gene?q=rpoB"\n+ rel="noreferrer noopener">rpoB</a>\n+ (1.0 p.Asp435Val)\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Ethambutol</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Pyrazinamide</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Streptomycin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Ethionamide</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Fluoroquinolones</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Amikacin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Capreomycin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Kanamycin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Para-aminosalicylic acid</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Linezolid</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Cycloserine</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Delamanid</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Clofazimine</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Bedaquiline</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Aminoglycosides</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Levofloxacin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Moxifloxacin</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ <tr>\n+ <td>Pretomanid</td>\n+ <td>S</td>\n+ <td></td>\n+ </tr>\n+ </table>\n+ </div>\n </div>\n <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"\n integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">\n' |
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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_drug_resistance_report.txt --- a/test-data/rif_resistant_drug_resistance_report.txt Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.txt Fri May 31 20:06:49 2024 +0000 |
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| @@ -1,10 +1,9 @@ #Rif_resistant Report -#Lineage Family Spoligotype RD Agreement -lineage2 East-Asian Beijing RD105 1.0 -lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0 -lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 1.0 +#Lineage Support Family RD +lineage2 0.9940119760479041 East-Asian RD105 +lineage2.2.2 1.0 East-Asian (Beijing) RD105;RD207 -#TBProfiler Drug Resistance Report +#TB-Profiler Drug Resistance Report #Drug Resistance Supporting Mutations Isoniazid S @@ -20,9 +19,12 @@ Para-aminosalicylic acid S Linezolid S Cycloserine S -Delaminid S +Delamanid S Clofazimine S Bedaquiline S Aminoglycosides S +Levofloxacin S +Moxifloxacin S +Pretomanid S -#Drug resistance predictions are for research purposes only and are produced by the TBProfiler software. +#Drug resistance predictions are for research purposes only and are produced by the TB-Profiler software. |
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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_variants_report.html --- a/test-data/rif_resistant_variants_report.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_variants_report.html Fri May 31 20:06:49 2024 +0000 |
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| b'@@ -22,10 +22,545 @@\n </h2>\n </div>\n <hr>\n- <div>\n- <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html"\n- target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p>\n- <p>Kindly check if the \'<strong>ANN</strong>\' field is present.</p>\n+ <div class="row justify-content-center align-items-center">\n+ <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">\n+ <thead class="thead-light">\n+ <tr>\n+ <th scope="col">CHR</th>\n+ <th scope="col">GENE</th>\n+ <th scope="col">LOCUS</th>\n+ <th scope="col">PRODUCT</th>\n+ <th scope="col">IS_SNV</th>\n+ <th scope="col">EFFECT</th>\n+ <th scope="col">POS</th>\n+ <th scope="col">REF</th>\n+ <th scope="col">ALT</th>\n+ <th scope="col">BIOTYPE</th>\n+ <th scope="col">NUCLEOTIDE</th>\n+ <th scope="col">CONSEQUENCE</th>\n+ <th scope="col">IMPACT</th>\n+ <th scope="col">PATHWAY</th>\n+ </tr>\n+ </thead>\n+ <tbody>\n+\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv0014c</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv0014c</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"\n+ target="_blank" rel="noreferrer noopener">15890</a>\n+ </td>\n+ <td>G</td>\n+ <td>A</td>\n+ <td>protein_coding</td>\n+ <td>c.1581C>T</td>\n+ <td>p.Ser527Ser</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv0127</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv0127</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"\n+ target="_blank" rel="noreferrer noopener">154990</a>\n+ </td>\n+ <td>G</td>\n+ <td>T</td>\n+ <td>protein_coding</td>\n+ <td>c.759G>T</td>\n+ <td>p.Arg253Arg</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv0284</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv0284</a>\n+ </td>\n+ <td>\n+ '..b'ue</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"\n+ target="_blank" rel="noreferrer noopener">3587446</a>\n+ </td>\n+ <td>G</td>\n+ <td>A</td>\n+ <td>protein_coding</td>\n+ <td>c.94C>T</td>\n+ <td>p.Leu32Leu</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv3799c</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv3799c</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"\n+ target="_blank" rel="noreferrer noopener">4254431</a>\n+ </td>\n+ <td>G</td>\n+ <td>A</td>\n+ <td>protein_coding</td>\n+ <td>c.1518C>T</td>\n+ <td>p.Asp506Asp</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv3799c</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv3799c</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>missense_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"\n+ target="_blank" rel="noreferrer noopener">4254477</a>\n+ </td>\n+ <td>T</td>\n+ <td>C</td>\n+ <td>protein_coding</td>\n+ <td>c.1472A>G</td>\n+ <td>p.His491Arg</td>\n+ <td>MODERATE</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ </tbody>\n+ <tfoot class="thead-light">\n+ <tr>\n+ <th scope="col">CHR</th>\n+ <th scope="col">GENE</th>\n+ <th scope="col">LOCUS</th>\n+ <th scope="col">PRODUCT</th>\n+ <th scope="col">TYPE</th>\n+ <th scope="col">EFFECT</th>\n+ <th scope="col">POS</th>\n+ <th scope="col">REF</th>\n+ <th scope="col">ALT</th>\n+ <th scope="col">BIOTYPE</th>\n+ <th scope="col">NUCLEOTIDE</th>\n+ <th scope="col">CONSEQUENCE</th>\n+ <th scope="col">IMPACT</th>\n+ <th scope="col">PATHWAY</th>\n+ </tr>\n+ </tfoot>\n+ </table>\n+</div>\n+</main>\n+<div class="mt-5">\n </div>\n <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"\n integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">\n' |
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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_variants_report.txt --- a/test-data/rif_resistant_variants_report.txt Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_variants_report.txt Fri May 31 20:06:49 2024 +0000 |
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| @@ -1,4 +1,22 @@ #Rif_resistant Report -#Lineage Family Spoligotype RD Agreement -#CHR GENE IDENTIFIER PRODUCT TYPE ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHAWAY +#CHR GENE IDENTIFIER PRODUCT IS_SNV ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHWAY +Chromosome Rv0014c GENE_Rv0014c NOPROTEIN True synonymous_variant 15890 G A p.Ser527Ser LOW +Chromosome Rv0127 GENE_Rv0127 NOPROTEIN True synonymous_variant 154990 G T p.Arg253Arg LOW +Chromosome Rv0284 GENE_Rv0284 NOPROTEIN True synonymous_variant 346693 G T p.Ser353Ser LOW +Chromosome Rv0372c GENE_Rv0372c NOPROTEIN True synonymous_variant 449194 G A p.Gly64Gly LOW +Chromosome Rv0411c GENE_Rv0411c NOPROTEIN True synonymous_variant 497491 G A p.Asp270Asp LOW +Chromosome Rv0667 GENE_Rv0667 NOPROTEIN True missense_variant 761110 A T p.Asp435Val MODERATE +Chromosome Rv0715 GENE_Rv0715 NOPROTEIN True synonymous_variant 811753 C T p.His4His LOW +Chromosome Rv1391 GENE_Rv1391 NOPROTEIN True synonymous_variant 1565566 C T p.Pro42Pro LOW +Chromosome Rv1630 GENE_Rv1630 NOPROTEIN True synonymous_variant 1834177 A C p.Arg212Arg LOW +Chromosome Rv1640c GENE_Rv1640c NOPROTEIN True synonymous_variant 1849051 C T p.Pro995Pro LOW +Chromosome Rv2231c GENE_Rv2231c NOPROTEIN True synonymous_variant 2505085 G A p.Ala205Ala LOW +Chromosome Rv2268c GENE_Rv2268c NOPROTEIN True synonymous_variant 2543395 T C p.Glu294Glu LOW +Chromosome Rv2357c GENE_Rv2357c NOPROTEIN True synonymous_variant 2640807 G A p.Val86Val LOW +Chromosome Rv2472 GENE_Rv2472 NOPROTEIN True synonymous_variant 2775361 C T p.Arg30Arg LOW +Chromosome Rv2483c GENE_Rv2483c NOPROTEIN True synonymous_variant 2789798 G T p.Arg409Arg LOW +Chromosome Rv3109 GENE_Rv3109 NOPROTEIN True synonymous_variant 3477942 A G p.Thr98Thr LOW +Chromosome Rv3210c GENE_Rv3210c NOPROTEIN True synonymous_variant 3587446 G A p.Leu32Leu LOW +Chromosome Rv3799c GENE_Rv3799c NOPROTEIN True synonymous_variant 4254431 G A p.Asp506Asp LOW +Chromosome Rv3799c GENE_Rv3799c NOPROTEIN True missense_variant 4254477 T C p.His491Arg MODERATE |
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| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_variants_report_with_lineage.html --- a/test-data/rif_resistant_variants_report_with_lineage.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_variants_report_with_lineage.html Fri May 31 20:06:49 2024 +0000 |
| b |
| b'@@ -21,6 +21,33 @@\n rif_resistant Report\n </h2>\n </div>\n+ <div class="row">\n+ <table class="table table-striped table-hover table-responsive-md">\n+ <caption>Lineage Info</caption>\n+ <thead class="thead-light">\n+ <tr>\n+ <th scope="col">Lineage</th>\n+ <th scope="col">Lineage support fraction</th>\n+ <th scope="col">Family</th>\n+ <th scope="col">RD</th>\n+ </tr>\n+ </thead>\n+ <tbody>\n+ <tr>\n+ <td>lineage2</td>\n+ <td>0.9940119760479041</td>\n+ <td>East-Asian</td>\n+ <td>RD105</td>\n+ </tr>\n+ <tr>\n+ <td>lineage2.2.2</td>\n+ <td>1.0</td>\n+ <td>East-Asian (Beijing)</td>\n+ <td>RD105;RD207</td>\n+ </tr>\n+ </tbody>\n+ </table>\n+ </div>\n <hr>\n <div class="row justify-content-center align-items-center">\n <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">\n@@ -35,33 +62,561 @@\n </thead>\n <tbody>\n <tr>\n- <td>lineage2</td>\n- <td>East-Asian</td>\n- <td>Beijing</td>\n- <td>RD105</td>\n- <td>1.0</td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n </tr>\n <tr>\n- <td>lineage2.2</td>\n- <td>East-Asian (Beijing)</td>\n- <td>Beijing-RD207</td>\n- <td>RD105;RD207</td>\n- <td>1.0</td>\n- </tr>\n- <tr>\n- <td>lineage2.2.2</td>\n- <td>East-Asian (Beijing)</td>\n- <td>Beijing-RD105/RD207</td>\n- <td>RD105;RD207</td>\n- <td>1.0</td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n+ <td></td>\n </tr>\n </tbody>\n </table>\n </div>\n-<div>\n- <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html"\n- target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p>\n- <p>Kindly check if the \'<strong>ANN</strong>\' field is present.</p>\n+<div class="row justify-content-center align-items-center">\n+ <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">\n+ <thead class="thead-light">\n+ <tr>\n+ <th scope="col">CHR</th>\n+ <th scope="col">GENE</th>\n+ <th scope="col">LOCUS</th>\n+ <th scope="col">PRODUCT</th>\n+ <th scope="col">IS_SNV</th>\n+ <th scope="col">EFFECT</th>\n+ <th scope="col">POS</th>\n+ <th scope="col">REF</th>\n+ <th scope="col">ALT</th>\n+ <th scope="col">BIOTYPE</th>\n+ <th scope="col">NUCLEOTIDE</th>\n+ <th scope="col">CONSEQUENCE</th>\n+ <th scope="col">IMPACT</th>\n+ <th scope="col">PATHWAY</th>\n+ </tr>\n+ </thead>\n+ <tbody>\n+\n+ <tr>\n+ <td>Chrom'..b'ue</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"\n+ target="_blank" rel="noreferrer noopener">3587446</a>\n+ </td>\n+ <td>G</td>\n+ <td>A</td>\n+ <td>protein_coding</td>\n+ <td>c.94C>T</td>\n+ <td>p.Leu32Leu</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv3799c</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv3799c</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>synonymous_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"\n+ target="_blank" rel="noreferrer noopener">4254431</a>\n+ </td>\n+ <td>G</td>\n+ <td>A</td>\n+ <td>protein_coding</td>\n+ <td>c.1518C>T</td>\n+ <td>p.Asp506Asp</td>\n+ <td>LOW</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ <tr>\n+ <td>Chromosome</td>\n+ <td>Rv3799c</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"\n+ rel="noreferrer noopener">GENE_Rv3799c</a>\n+ </td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ <td>True</td>\n+ <td>missense_variant</td>\n+ <td>\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"\n+ target="_blank" rel="noreferrer noopener">4254477</a>\n+ </td>\n+ <td>T</td>\n+ <td>C</td>\n+ <td>protein_coding</td>\n+ <td>c.1472A>G</td>\n+ <td>p.His491Arg</td>\n+ <td>MODERATE</td>\n+ <td>\n+ <p>NA</p>\n+ </td>\n+ </tr>\n+ </tbody>\n+ <tfoot class="thead-light">\n+ <tr>\n+ <th scope="col">CHR</th>\n+ <th scope="col">GENE</th>\n+ <th scope="col">LOCUS</th>\n+ <th scope="col">PRODUCT</th>\n+ <th scope="col">TYPE</th>\n+ <th scope="col">EFFECT</th>\n+ <th scope="col">POS</th>\n+ <th scope="col">REF</th>\n+ <th scope="col">ALT</th>\n+ <th scope="col">BIOTYPE</th>\n+ <th scope="col">NUCLEOTIDE</th>\n+ <th scope="col">CONSEQUENCE</th>\n+ <th scope="col">IMPACT</th>\n+ <th scope="col">PATHWAY</th>\n+ </tr>\n+ </tfoot>\n+ </table>\n+</div>\n+</main>\n+<div class="mt-5">\n </div>\n <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"\n integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">\n' |
| b |
| diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_variants_report_with_lineage.txt --- a/test-data/rif_resistant_variants_report_with_lineage.txt Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_variants_report_with_lineage.txt Fri May 31 20:06:49 2024 +0000 |
| b |
| @@ -1,7 +1,25 @@ #Rif_resistant Report -#Lineage Family Spoligotype RD Agreement -lineage2 East-Asian Beijing RD105 1.0 -lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0 -lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 1.0 +#Lineage Support Family RD +lineage2 0.9940119760479041 East-Asian RD105 +lineage2.2.2 1.0 East-Asian (Beijing) RD105;RD207 -#CHR GENE IDENTIFIER PRODUCT TYPE ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHAWAY +#CHR GENE IDENTIFIER PRODUCT IS_SNV ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHWAY +Chromosome Rv0014c GENE_Rv0014c NOPROTEIN True synonymous_variant 15890 G A p.Ser527Ser LOW +Chromosome Rv0127 GENE_Rv0127 NOPROTEIN True synonymous_variant 154990 G T p.Arg253Arg LOW +Chromosome Rv0284 GENE_Rv0284 NOPROTEIN True synonymous_variant 346693 G T p.Ser353Ser LOW +Chromosome Rv0372c GENE_Rv0372c NOPROTEIN True synonymous_variant 449194 G A p.Gly64Gly LOW +Chromosome Rv0411c GENE_Rv0411c NOPROTEIN True synonymous_variant 497491 G A p.Asp270Asp LOW +Chromosome Rv0667 GENE_Rv0667 NOPROTEIN True missense_variant 761110 A T p.Asp435Val MODERATE +Chromosome Rv0715 GENE_Rv0715 NOPROTEIN True synonymous_variant 811753 C T p.His4His LOW +Chromosome Rv1391 GENE_Rv1391 NOPROTEIN True synonymous_variant 1565566 C T p.Pro42Pro LOW +Chromosome Rv1630 GENE_Rv1630 NOPROTEIN True synonymous_variant 1834177 A C p.Arg212Arg LOW +Chromosome Rv1640c GENE_Rv1640c NOPROTEIN True synonymous_variant 1849051 C T p.Pro995Pro LOW +Chromosome Rv2231c GENE_Rv2231c NOPROTEIN True synonymous_variant 2505085 G A p.Ala205Ala LOW +Chromosome Rv2268c GENE_Rv2268c NOPROTEIN True synonymous_variant 2543395 T C p.Glu294Glu LOW +Chromosome Rv2357c GENE_Rv2357c NOPROTEIN True synonymous_variant 2640807 G A p.Val86Val LOW +Chromosome Rv2472 GENE_Rv2472 NOPROTEIN True synonymous_variant 2775361 C T p.Arg30Arg LOW +Chromosome Rv2483c GENE_Rv2483c NOPROTEIN True synonymous_variant 2789798 G T p.Arg409Arg LOW +Chromosome Rv3109 GENE_Rv3109 NOPROTEIN True synonymous_variant 3477942 A G p.Thr98Thr LOW +Chromosome Rv3210c GENE_Rv3210c NOPROTEIN True synonymous_variant 3587446 G A p.Leu32Leu LOW +Chromosome Rv3799c GENE_Rv3799c NOPROTEIN True synonymous_variant 4254431 G A p.Asp506Asp LOW +Chromosome Rv3799c GENE_Rv3799c NOPROTEIN True missense_variant 4254477 T C p.His491Arg MODERATE |
| b |
| diff -r 4934c0ac6197 -r 42818629ec4c test-data/vcf_with_no_protein_report.html --- a/test-data/vcf_with_no_protein_report.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/vcf_with_no_protein_report.html Fri May 31 20:06:49 2024 +0000 |
| b |
| b'@@ -30,7 +30,7 @@\n <th scope="col">GENE</th>\n <th scope="col">LOCUS</th>\n <th scope="col">PRODUCT</th>\n- <th scope="col">TYPE</th>\n+ <th scope="col">IS_SNV</th>\n <th scope="col">EFFECT</th>\n <th scope="col">POS</th>\n <th scope="col">REF</th>\n@@ -55,10 +55,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O69720"\n target="_blank" rel="noreferrer noopener">O69720</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..4200220&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..4200220"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..None"\n target="_blank" rel="noreferrer noopener">4200220</a>\n </td>\n <td>G</td>\n@@ -82,10 +82,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O69722"\n target="_blank" rel="noreferrer noopener">O69722</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>synonymous_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..4202383&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..4202383"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..None"\n target="_blank" rel="noreferrer noopener">4202383</a>\n </td>\n <td>C</td>\n@@ -114,10 +114,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O69725"\n target="_blank" rel="noreferrer noopener">O69725</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..4205120&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..4205120"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..None"\n target="_blank" rel="noreferrer noopener">4205120</a>\n </td>\n <td>G</td>\n@@ -146,10 +146,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O69729"\n target="_blank" rel="noreferrer noopener">O69729</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..4210876&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..4210876"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..None"\n target="_blank" rel="noreferrer noopener">4210876</a>\n </td>\n <td>C</td>\n@@ -173,10 +173,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=P72036"\n target="_blank" rel="noreferrer noopener">P72036</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n'..b' <td>A</td>\n@@ -459,10 +459,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7"\n target="_blank" rel="noreferrer noopener">P9WNL7</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..4247646&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..4247646"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..None"\n target="_blank" rel="noreferrer noopener">4247646</a>\n </td>\n <td>C</td>\n@@ -491,10 +491,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O53577"\n target="_blank" rel="noreferrer noopener">O53577</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>synonymous_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..4251297&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..4251297"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..None"\n target="_blank" rel="noreferrer noopener">4251297</a>\n </td>\n <td>C</td>\n@@ -517,10 +517,10 @@\n <td>\n <p>NA</p>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..4254290&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..4254290"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..None"\n target="_blank" rel="noreferrer noopener">4254290</a>\n </td>\n <td>T</td>\n@@ -544,10 +544,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O53578"\n target="_blank" rel="noreferrer noopener">O53578</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..4254478&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..4254478"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..None"\n target="_blank" rel="noreferrer noopener">4254478</a>\n </td>\n <td>G</td>\n@@ -571,10 +571,10 @@\n <a href="https://explorer.sanbi.ac.za/search?q=O53580"\n target="_blank" rel="noreferrer noopener">O53580</a>\n </td>\n- <td>snp</td>\n+ <td>True</td>\n <td>missense_variant</td>\n <td>\n- <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..4261499&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..4261499"\n+ <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..None"\n target="_blank" rel="noreferrer noopener">4261499</a>\n </td>\n <td>A</td>\n' |
| b |
| diff -r 4934c0ac6197 -r 42818629ec4c test-data/vcf_with_no_protein_report.txt --- a/test-data/vcf_with_no_protein_report.txt Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/vcf_with_no_protein_report.txt Fri May 31 20:06:49 2024 +0000 |
| b |
| @@ -1,22 +1,21 @@ #Vcf_with_no_protein Report -#Lineage Family Spoligotype RD Agreement -#CHR GENE IDENTIFIER PRODUCT TYPE ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHWAY -Chromosome Rv3753c Rv3753c O69720 snp missense_variant 4200220 G A p.Thr1Met MODERATE -Chromosome Rv3756c Rv3756c O69722 snp synonymous_variant 4202383 C A p.Val77Val LOW ABC transporters -Chromosome Rv3759c Rv3759c O69725 snp missense_variant 4205120 G A p.Pro85Leu MODERATE ABC transporters -Chromosome Rv3764c Rv3764c O69729 snp missense_variant 4210876 C T p.Arg45His MODERATE -Chromosome Rv3769 Rv3769 P72036 snp missense_variant 4214747 C T p.His45Tyr MODERATE -Chromosome Rv3770c Rv3770c P72037 snp missense_variant 4215484 C G p.Ala98Pro MODERATE -Chromosome Rv3772 Rv3772 P9WML5 snp missense_variant 4217557 G A p.Ala142Thr MODERATE Phenylalanine, tyrosine and tryptophan biosynthesis,Phenylalanine metabolism,Histidine metabolism,Tyrosine metabolism -Chromosome Rv3777 Rv3777 P72043 snp missense_variant 4223172 C T p.Ala160Val MODERATE -Chromosome Rv3785 Rv3785 P9WKX1 snp synonymous_variant 4232327 G A p.Arg336Arg LOW -Chromosome Rv3792 Rv3792 P9WN03 snp synonymous_variant 4238963 C T p.His344His LOW Arabinogalactan biosynthesis - Mycobacterium -Chromosome Rv3792 Rv3792 P9WN03 snp missense_variant 4239274 C G p.Pro448Arg MODERATE Arabinogalactan biosynthesis - Mycobacterium -Chromosome Rv3793 Rv3793 P9WNL5 snp missense_variant 4240671 T C p.Ile270Thr MODERATE Lipoarabinomannan (LAM) biosynthesis -Chromosome Rv3795 Rv3795 P9WNL7 snp missense_variant 4247429 A G p.Met306Val MODERATE Arabinogalactan biosynthesis - Mycobacterium -Chromosome Rv3795 Rv3795 P9WNL7 snp missense_variant 4247646 C A p.Ala378Glu MODERATE Arabinogalactan biosynthesis - Mycobacterium -Chromosome Rv3797 Rv3797 O53577 snp synonymous_variant 4251297 C G p.Gly71Gly LOW -Chromosome Rv3798 Rv3798 NOPROTEIN snp missense_variant 4254290 T G p.Leu433Arg MODERATE -Chromosome Rv3799c Rv3799c O53578 snp missense_variant 4254478 G A p.His491Tyr MODERATE -Chromosome Rv3801c Rv3801c O53580 snp missense_variant 4261499 A G p.Val523Ala MODERATE +#CHR GENE IDENTIFIER PRODUCT IS_SNV ANNOTATION POS REF ALT CONSEQUENCE IMPACT PATHWAY +Chromosome Rv3753c Rv3753c O69720 True missense_variant 4200220 G A p.Thr1Met MODERATE +Chromosome Rv3756c Rv3756c O69722 True synonymous_variant 4202383 C A p.Val77Val LOW ABC transporters +Chromosome Rv3759c Rv3759c O69725 True missense_variant 4205120 G A p.Pro85Leu MODERATE ABC transporters +Chromosome Rv3764c Rv3764c O69729 True missense_variant 4210876 C T p.Arg45His MODERATE +Chromosome Rv3769 Rv3769 P72036 True missense_variant 4214747 C T p.His45Tyr MODERATE +Chromosome Rv3770c Rv3770c P72037 True missense_variant 4215484 C G p.Ala98Pro MODERATE +Chromosome Rv3772 Rv3772 P9WML5 True missense_variant 4217557 G A p.Ala142Thr MODERATE Phenylalanine, tyrosine and tryptophan biosynthesis,Phenylalanine metabolism,Histidine metabolism,Tyrosine metabolism +Chromosome Rv3777 Rv3777 P72043 True missense_variant 4223172 C T p.Ala160Val MODERATE +Chromosome Rv3785 Rv3785 P9WKX1 True synonymous_variant 4232327 G A p.Arg336Arg LOW +Chromosome Rv3792 Rv3792 P9WN03 True synonymous_variant 4238963 C T p.His344His LOW Arabinogalactan biosynthesis - Mycobacterium +Chromosome Rv3792 Rv3792 P9WN03 True missense_variant 4239274 C G p.Pro448Arg MODERATE Arabinogalactan biosynthesis - Mycobacterium +Chromosome Rv3793 Rv3793 P9WNL5 True missense_variant 4240671 T C p.Ile270Thr MODERATE Lipoarabinomannan (LAM) biosynthesis +Chromosome Rv3795 Rv3795 P9WNL7 True missense_variant 4247429 A G p.Met306Val MODERATE Arabinogalactan biosynthesis - Mycobacterium +Chromosome Rv3795 Rv3795 P9WNL7 True missense_variant 4247646 C A p.Ala378Glu MODERATE Arabinogalactan biosynthesis - Mycobacterium +Chromosome Rv3797 Rv3797 O53577 True synonymous_variant 4251297 C G p.Gly71Gly LOW +Chromosome Rv3798 Rv3798 NOPROTEIN True missense_variant 4254290 T G p.Leu433Arg MODERATE +Chromosome Rv3799c Rv3799c O53578 True missense_variant 4254478 G A p.His491Tyr MODERATE +Chromosome Rv3801c Rv3801c O53580 True missense_variant 4261499 A G p.Val523Ala MODERATE |