Mercurial > repos > iuc > tbvcfreport
changeset 2:4934c0ac6197 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
| author | iuc |
|---|---|
| date | Thu, 17 Mar 2022 07:33:00 +0000 |
| parents | adc0645b945c |
| children | |
| files | tbvcfreport.xml test-data/rif_resistant_drug_resistance_report.html test-data/rif_resistant_drug_resistance_report.txt test-data/vcf_with_no_protein.vcf test-data/vcf_with_no_protein_report.html test-data/vcf_with_no_protein_report.txt |
| diffstat | 6 files changed, 789 insertions(+), 4 deletions(-) [+] |
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--- a/tbvcfreport.xml Wed Jul 07 09:22:44 2021 +0000 +++ b/tbvcfreport.xml Thu Mar 17 07:33:00 2022 +0000 @@ -2,7 +2,7 @@ <tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0"> <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description> <macros> - <token name="@TOOL_VERSION@">0.1.8</token> + <token name="@TOOL_VERSION@">0.1.10</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement> @@ -64,7 +64,7 @@ <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" /> <section name="adv" title="Advanced options" expanded="false"> - <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify on-premise COMBAT-TB-NeoDB URI" help="For people with an on-premise deployment of COMBAT-TB-NeoDB" /> + <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> </inputs> <outputs> @@ -78,12 +78,12 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" /> <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" /> </test> - <test> + <test expect_num_outputs="4"> <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" /> <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.html" ftype="html" /> @@ -91,6 +91,12 @@ <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" /> <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" /> </test> + <test expect_num_outputs="2"> + <!-- test for bug fixed in 0.1.9 onwards: a gene with no protein product --> + <param name="input_vcf" value="vcf_with_no_protein.vcf" ftype="vcf" /> + <output name="variants_report_html" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.html" ftype="html" /> + <output name="variants_report_txt" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.txt" ftype="txt" /> + </test> </tests> <help> <![CDATA[
--- a/test-data/rif_resistant_drug_resistance_report.html Wed Jul 07 09:22:44 2021 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.html Thu Mar 17 07:33:00 2022 +0000 @@ -127,6 +127,13 @@ <td>S</td> <td></td> </tr> + </tr> + <tr> + <td>Aminoglycosides</td> + <td>S</td> + <td></td> + </tr> + </table> </div> <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
--- a/test-data/rif_resistant_drug_resistance_report.txt Wed Jul 07 09:22:44 2021 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.txt Thu Mar 17 07:33:00 2022 +0000 @@ -23,5 +23,6 @@ Delaminid S Clofazimine S Bedaquiline S +Aminoglycosides S #Drug resistance predictions are for research purposes only and are produced by the TBProfiler software.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_with_no_protein.vcf Thu Mar 17 07:33:00 2022 +0000 @@ -0,0 +1,88 @@ +##fileformat=VCFv4.2 +##fileDate=20220316 +##source=freeBayes v1.1.0-dirty +##reference=reference/ref.fa +##contig=<ID=Chromosome,length=4411532> +##phasing=none +##commandline="freebayes -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam --region Chromosome:0-1121280" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype."> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype."> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##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"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##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=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> +##filter=/usr/local/tools/_conda/envs/__snippy@3.2/bin/snippy-vcf_filter --minqual 10 --mincov 10 --minfrac 0.9 snps.raw.vcf +##SnpEffVersion="4.3 (build 2016-07-03 08:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -no-downstream -no-upstream -no-intergenic -no-utr -noStats ref snps.filt.vcf " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT snps +Chromosome 4198611 . CGGGGGT CGGGGT 6312.89 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1M1D5M;DP=194;DPB=182.429;DPRA=0;EPP=3.11156;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1453.6;PAIRED=0.989637;PAIREDR=0;PAO=19;PQA=553.5;PQR=355.5;PRO=13;QA=6821;QR=0;RO=0;RPL=100;RPP=3.56161;RPPR=0;RPR=93;RUN=1;SAF=96;SAP=3.02155;SAR=97;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,193:0:0:193:6821:-631.289,0 +Chromosome 4200220 . G A 7422.62 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=234;CIGAR=1X;DP=234;DPB=234;DPRA=0;EPP=6.72222;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1709.12;PAIRED=0.991453;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8248;QR=0;RO=0;RPL=108;RPP=6.01695;RPPR=0;RPR=126;RUN=1;SAF=123;SAP=4.34659;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3753c|Rv3753c|transcript|TRANSCRIPT_Rv3753c|protein_coding|1/1|c.2C>T|p.Thr1Met|2/501|2/501|1/166||WARNING_TRANSCRIPT_NO_START_CODON GT:DP:AD:RO:QR:AO:QA:GL 1:234:0,234:0:0:234:8248:-742.262,0 +Chromosome 4202383 . C A 4389.44 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=137;CIGAR=1X;DP=137;DPB=137;DPRA=0;EPP=3.02615;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1010.7;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4876;QR=0;RO=0;RPL=65;RPP=3.78696;RPPR=0;RPR=72;RUN=1;SAF=74;SAP=4.92817;SAR=63;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3756c|Rv3756c|transcript|TRANSCRIPT_Rv3756c|protein_coding|1/1|c.231G>T|p.Val77Val|231/720|231/720|77/239|| GT:DP:AD:RO:QR:AO:QA:GL 1:137:0,137:0:0:137:4876:-438.944,0 +Chromosome 4205120 . G A 5602.51 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=177;CIGAR=1X;DP=178;DPB=178;DPRA=0;EPP=14.8;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1290.03;PAIRED=0.988701;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6248;QR=21;RO=1;RPL=80;RPP=6.55581;RPPR=5.18177;RPR=97;RUN=1;SAF=89;SAP=3.02257;SAR=88;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3759c|Rv3759c|transcript|TRANSCRIPT_Rv3759c|protein_coding|1/1|c.254C>T|p.Pro85Leu|254/948|254/948|85/315|| GT:DP:AD:RO:QR:AO:QA:GL 1:178:1,177:1:21:177:6248:-560.251,0 +Chromosome 4210876 . C T 8084.63 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=256;CIGAR=1X;DP=256;DPB=256;DPRA=0;EPP=4.23175;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1861.55;PAIRED=0.996094;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8984;QR=0;RO=0;RPL=139;RPP=7.11574;RPPR=0;RPR=117;RUN=1;SAF=117;SAP=7.11574;SAR=139;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3764c|Rv3764c|transcript|TRANSCRIPT_Rv3764c|protein_coding|1/1|c.134G>A|p.Arg45His|134/1428|134/1428|45/475|| GT:DP:AD:RO:QR:AO:QA:GL 1:256:0,256:0:0:256:8984:-808.463,0 +Chromosome 4214747 . C T 6141.11 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=194;CIGAR=1X;DP=194;DPB=194;DPRA=0;EPP=3.41325;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1414.04;PAIRED=0.994845;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6823;QR=0;RO=0;RPL=114;RPP=15.9496;RPPR=0;RPR=80;RUN=1;SAF=98;SAP=3.05507;SAR=96;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3769|Rv3769|transcript|TRANSCRIPT_Rv3769|protein_coding|1/1|c.133C>T|p.His45Tyr|133/273|133/273|45/90|| GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,194:0:0:194:6823:-614.111,0 +Chromosome 4215484 . C G 7180.37 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=225;CIGAR=1X;DP=225;DPB=225;DPRA=0;EPP=3.4832;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1653.34;PAIRED=0.991111;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7979;QR=0;RO=0;RPL=111;RPP=3.09716;RPPR=0;RPR=114;RUN=1;SAF=102;SAP=7.26639;SAR=123;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3770c|Rv3770c|transcript|TRANSCRIPT_Rv3770c|protein_coding|1/1|c.292G>C|p.Ala98Pro|292/576|292/576|98/191|| GT:DP:AD:RO:QR:AO:QA:GL 1:225:0,225:0:0:225:7979:-718.037,0 +Chromosome 4216255 . G C 6090.49 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1X;DP=193;DPB=193;DPRA=0;EPP=7.07197;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1402.39;PAIRED=0.974093;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6767;QR=0;RO=0;RPL=99;RPP=3.29158;RPPR=0;RPR=94;RUN=1;SAF=89;SAP=5.54181;SAR=104;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1:193:0,193:0:0:193:6767:-609.049,0 +Chromosome 4217557 . G A 4628.62 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=147;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=4.20683;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1065.78;PAIRED=0.993197;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5142;QR=0;RO=0;RPL=78;RPP=4.20683;RPPR=0;RPR=69;RUN=1;SAF=76;SAP=3.3796;SAR=71;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3772|Rv3772|transcript|TRANSCRIPT_Rv3772|protein_coding|1/1|c.424G>A|p.Ala142Thr|424/1062|424/1062|142/353|| GT:DP:AD:RO:QR:AO:QA:GL 1:147:0,147:0:0:147:5142:-462.862,0 +Chromosome 4223172 . C T 3477.35 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=110;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=18.487;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=800.69;PAIRED=0.981818;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3862;QR=0;RO=0;RPL=41;RPP=18.487;RPPR=0;RPR=69;RUN=1;SAF=28;SAP=60.5741;SAR=82;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3777|Rv3777|transcript|TRANSCRIPT_Rv3777|protein_coding|1/1|c.479C>T|p.Ala160Val|479/987|479/987|160/328|| GT:DP:AD:RO:QR:AO:QA:GL 1:110:0,110:0:0:110:3862:-347.735,0 +Chromosome 4232327 . G A 7703.92 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=242;CIGAR=1X;DP=243;DPB=243;DPRA=0;EPP=5.91756;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1773.89;PAIRED=0.995868;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8565;QR=0;RO=0;RPL=135;RPP=10.0452;RPPR=0;RPR=107;RUN=1;SAF=113;SAP=5.30739;SAR=129;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3785|Rv3785|transcript|TRANSCRIPT_Rv3785|protein_coding|1/1|c.1008G>A|p.Arg336Arg|1008/1074|1008/1074|336/357|| GT:DP:AD:RO:QR:AO:QA:GL 1:243:0,242:0:0:242:8565:-770.392,0 +Chromosome 4238963 . C T 6583.6 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=214;CIGAR=1X;DP=216;DPB=216;DPRA=0;EPP=7.92148;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1515.93;PAIRED=0.985981;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7378;QR=60;RO=2;RPL=101;RPP=4.47148;RPPR=7.35324;RPR=113;RUN=1;SAF=99;SAP=5.60795;SAR=115;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3792|Rv3792|transcript|TRANSCRIPT_Rv3792|protein_coding|1/1|c.1032C>T|p.His344His|1032/1932|1032/1932|344/643|| GT:DP:AD:RO:QR:AO:QA:GL 1:216:2,214:2:60:214:7378:-658.36,0 +Chromosome 4239274 . C G 7506.51 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=238;CIGAR=1X;DP=238;DPB=238;DPRA=0;EPP=7.42624;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1728.44;PAIRED=0.995798;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8341;QR=0;RO=0;RPL=124;RPP=3.92268;RPPR=0;RPR=114;RUN=1;SAF=116;SAP=3.33876;SAR=122;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3792|Rv3792|transcript|TRANSCRIPT_Rv3792|protein_coding|1/1|c.1343C>G|p.Pro448Arg|1343/1932|1343/1932|448/643|| GT:DP:AD:RO:QR:AO:QA:GL 1:238:0,238:0:0:238:8341:-750.651,0 +Chromosome 4240671 . T C 6428.63 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=203;CIGAR=1X;DP=203;DPB=203;DPRA=0;EPP=5.4171;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1480.25;PAIRED=0.980296;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7143;QR=0;RO=0;RPL=89;RPP=9.69587;RPPR=0;RPR=114;RUN=1;SAF=92;SAP=6.87188;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3793|Rv3793|transcript|TRANSCRIPT_Rv3793|protein_coding|1/1|c.809T>C|p.Ile270Thr|809/3285|809/3285|270/1094|| GT:DP:AD:RO:QR:AO:QA:GL 1:203:0,203:0:0:203:7143:-642.863,0 +Chromosome 4247429 . A G 6696.64 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=211;CIGAR=1X;DP=212;DPB=212;DPRA=0;EPP=5.32585;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1541.96;PAIRED=0.990521;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7445;QR=0;RO=0;RPL=118;RPP=9.44239;RPPR=0;RPR=93;RUN=1;SAF=99;SAP=4.74954;SAR=112;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3795|Rv3795|transcript|TRANSCRIPT_Rv3795|protein_coding|1/1|c.916A>G|p.Met306Val|916/3297|916/3297|306/1098|| GT:DP:AD:RO:QR:AO:QA:GL 1:212:0,211:0:0:211:7445:-669.664,0 +Chromosome 4247646 . C A 6787.39 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=223;CIGAR=1X;DP=224;DPB=224;DPRA=0;EPP=9.09627;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1562.85;PAIRED=0.982063;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7580;QR=35;RO=1;RPL=106;RPP=4.18854;RPPR=5.18177;RPR=117;RUN=1;SAF=120;SAP=5.82445;SAR=103;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3795|Rv3795|transcript|TRANSCRIPT_Rv3795|protein_coding|1/1|c.1133C>A|p.Ala378Glu|1133/3297|1133/3297|378/1098|| GT:DP:AD:RO:QR:AO:QA:GL 1:224:1,223:1:35:223:7580:-678.739,0 +Chromosome 4251297 . C G 6197.38 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1X;DP=194;DPB=194;DPRA=0;EPP=3.29158;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1427;PAIRED=0.984456;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6891;QR=0;RO=0;RPL=96;RPP=3.02155;RPPR=0;RPR=97;RUN=1;SAF=91;SAP=4.37169;SAR=102;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3797|Rv3797|transcript|TRANSCRIPT_Rv3797|protein_coding|1/1|c.213C>G|p.Gly71Gly|213/1782|213/1782|71/593|| GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,193:0:0:193:6891:-619.738,0 +Chromosome 4254290 . T G 2461.94 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=79;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=12.9331;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=566.884;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2733;QR=0;RO=0;RPL=0;RPP=174.557;RPPR=0;RPR=79;RUN=1;SAF=30;SAP=12.9331;SAR=49;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3798|Rv3798|transcript|TRANSCRIPT_Rv3798|protein_coding|1/1|c.1298T>G|p.Leu433Arg|1298/1335|1298/1335|433/444|| GT:DP:AD:RO:QR:AO:QA:GL 1:79:0,79:0:0:79:2733:-246.194,0 +Chromosome 4254478 . G A 7180.38 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=227;CIGAR=1X;DP=227;DPB=227;DPRA=0;EPP=3.09639;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1653.34;PAIRED=0.986784;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7979;QR=0;RO=0;RPL=103;RPP=7.22889;RPPR=0;RPR=124;RUN=1;SAF=135;SAP=20.6978;SAR=92;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3799c|Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1471C>T|p.His491Tyr|1471/1569|1471/1569|491/522|| GT:DP:AD:RO:QR:AO:QA:GL 1:227:0,227:0:0:227:7979:-718.038,0 +Chromosome 4261499 . A G 5307.9 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=171;CIGAR=1X;DP=171;DPB=171;DPRA=0;EPP=7.59452;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1222.19;PAIRED=0.982456;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5897;QR=0;RO=0;RPL=88;RPP=3.32777;RPPR=0;RPR=83;RUN=1;SAF=83;SAP=3.32777;SAR=88;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3801c|Rv3801c|transcript|TRANSCRIPT_Rv3801c|protein_coding|1/1|c.1568T>C|p.Val523Ala|1568/1914|1568/1914|523/637|| GT:DP:AD:RO:QR:AO:QA:GL 1:171:0,171:0:0:171:5897:-530.79,0 +Chromosome 4263279 . G A 6207.29 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=196;CIGAR=1X;DP=198;DPB=198;DPRA=0;EPP=9.39177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1429.28;PAIRED=0.994898;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6971;QR=70;RO=2;RPL=100;RPP=3.18756;RPPR=7.35324;RPR=96;RUN=1;SAF=102;SAP=3.71935;SAR=94;SRF=1;SRP=3.0103;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1:198:2,196:2:70:196:6971:-620.729,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_with_no_protein_report.html Thu Mar 17 07:33:00 2022 +0000 @@ -0,0 +1,661 @@ +<!DOCTYPE html> +<html> + +<head> + <title></title> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> + <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" rel="stylesheet" + integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous"> + <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.bootstrap4.min.css"> + <link rel="stylesheet" type="text/css" + href="https://cdn.datatables.net/buttons/1.5.2/css/buttons.dataTables.min.css"> + </head> + +<body> + <div class="container"> + <div class="row"> + <h2 class="mt-5"> + vcf_with_no_protein Report + </h2> + </div> + <hr> + <div class="row justify-content-center align-items-center"> + <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0"> + <thead class="thead-light"> + <tr> + <th scope="col">CHR</th> + <th scope="col">GENE</th> + <th scope="col">LOCUS</th> + <th scope="col">PRODUCT</th> + <th scope="col">TYPE</th> + <th scope="col">EFFECT</th> + <th scope="col">POS</th> + <th scope="col">REF</th> + <th scope="col">ALT</th> + <th scope="col">BIOTYPE</th> + <th scope="col">NUCLEOTIDE</th> + <th scope="col">CONSEQUENCE</th> + <th scope="col">IMPACT</th> + <th scope="col">PATHWAY</th> + </tr> + </thead> + <tbody> + + <tr> + <td>Chromosome</td> + <td>Rv3753c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3753c" target="_blank" + rel="noreferrer noopener">Rv3753c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O69720" + target="_blank" rel="noreferrer noopener">O69720</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..4200220&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..4200220" + target="_blank" rel="noreferrer noopener">4200220</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.2C>T</td> + <td>p.Thr1Met</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3756c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3756c" target="_blank" + rel="noreferrer noopener">Rv3756c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O69722" + target="_blank" rel="noreferrer noopener">O69722</a> + </td> + <td>snp</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..4202383&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..4202383" + target="_blank" rel="noreferrer noopener">4202383</a> + </td> + <td>C</td> + <td>A</td> + <td>protein_coding</td> + <td>c.231G>T</td> + <td>p.Val77Val</td> + <td>LOW</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank" + rel="noreferrer noopener">ABC transporters</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3759c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3759c" target="_blank" + rel="noreferrer noopener">Rv3759c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O69725" + target="_blank" rel="noreferrer noopener">O69725</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..4205120&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..4205120" + target="_blank" rel="noreferrer noopener">4205120</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.254C>T</td> + <td>p.Pro85Leu</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu02010" target="_blank" + rel="noreferrer noopener">ABC transporters</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3764c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3764c" target="_blank" + rel="noreferrer noopener">Rv3764c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O69729" + target="_blank" rel="noreferrer noopener">O69729</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..4210876&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..4210876" + target="_blank" rel="noreferrer noopener">4210876</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.134G>A</td> + <td>p.Arg45His</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3769</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3769" target="_blank" + rel="noreferrer noopener">Rv3769</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P72036" + target="_blank" rel="noreferrer noopener">P72036</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..4214747&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..4214747" + target="_blank" rel="noreferrer noopener">4214747</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.133C>T</td> + <td>p.His45Tyr</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3770c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3770c" target="_blank" + rel="noreferrer noopener">Rv3770c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P72037" + target="_blank" rel="noreferrer noopener">P72037</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..4215484&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..4215484" + target="_blank" rel="noreferrer noopener">4215484</a> + </td> + <td>C</td> + <td>G</td> + <td>protein_coding</td> + <td>c.292G>C</td> + <td>p.Ala98Pro</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3772</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3772" target="_blank" + rel="noreferrer noopener">Rv3772</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WML5" + target="_blank" rel="noreferrer noopener">P9WML5</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..4217557&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..4217557" + target="_blank" rel="noreferrer noopener">4217557</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.424G>A</td> + <td>p.Ala142Thr</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00400" target="_blank" + rel="noreferrer noopener">Phenylalanine, tyrosine and tryptophan biosynthesis</a> + </small> + </p> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00360" target="_blank" + rel="noreferrer noopener">Phenylalanine metabolism</a> + </small> + </p> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00340" target="_blank" + rel="noreferrer noopener">Histidine metabolism</a> + </small> + </p> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00350" target="_blank" + rel="noreferrer noopener">Tyrosine metabolism</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3777</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3777" target="_blank" + rel="noreferrer noopener">Rv3777</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P72043" + target="_blank" rel="noreferrer noopener">P72043</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..4223172&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..4223172" + target="_blank" rel="noreferrer noopener">4223172</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.479C>T</td> + <td>p.Ala160Val</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3785</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3785" target="_blank" + rel="noreferrer noopener">Rv3785</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WKX1" + target="_blank" rel="noreferrer noopener">P9WKX1</a> + </td> + <td>snp</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..4232327&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..4232327" + target="_blank" rel="noreferrer noopener">4232327</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.1008G>A</td> + <td>p.Arg336Arg</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3792</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank" + rel="noreferrer noopener">Rv3792</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WN03" + target="_blank" rel="noreferrer noopener">P9WN03</a> + </td> + <td>snp</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..4238963&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..4238963" + target="_blank" rel="noreferrer noopener">4238963</a> + </td> + <td>C</td> + <td>T</td> + <td>protein_coding</td> + <td>c.1032C>T</td> + <td>p.His344His</td> + <td>LOW</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" + rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3792</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3792" target="_blank" + rel="noreferrer noopener">Rv3792</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WN03" + target="_blank" rel="noreferrer noopener">P9WN03</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..4239274&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..4239274" + target="_blank" rel="noreferrer noopener">4239274</a> + </td> + <td>C</td> + <td>G</td> + <td>protein_coding</td> + <td>c.1343C>G</td> + <td>p.Pro448Arg</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" + rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3793</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3793" target="_blank" + rel="noreferrer noopener">Rv3793</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WNL5" + target="_blank" rel="noreferrer noopener">P9WNL5</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..4240671&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..4240671" + target="_blank" rel="noreferrer noopener">4240671</a> + </td> + <td>T</td> + <td>C</td> + <td>protein_coding</td> + <td>c.809T>C</td> + <td>p.Ile270Thr</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00571" target="_blank" + rel="noreferrer noopener">Lipoarabinomannan (LAM) biosynthesis</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3795</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank" + rel="noreferrer noopener">Rv3795</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7" + target="_blank" rel="noreferrer noopener">P9WNL7</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..4247429&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..4247429" + target="_blank" rel="noreferrer noopener">4247429</a> + </td> + <td>A</td> + <td>G</td> + <td>protein_coding</td> + <td>c.916A>G</td> + <td>p.Met306Val</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" + rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3795</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3795" target="_blank" + rel="noreferrer noopener">Rv3795</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7" + target="_blank" rel="noreferrer noopener">P9WNL7</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..4247646&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..4247646" + target="_blank" rel="noreferrer noopener">4247646</a> + </td> + <td>C</td> + <td>A</td> + <td>protein_coding</td> + <td>c.1133C>A</td> + <td>p.Ala378Glu</td> + <td>MODERATE</td> + <td> + <p> + <small> + <a href="http://www.genome.jp/dbget-bin/www_bget?mtu00572" target="_blank" + rel="noreferrer noopener">Arabinogalactan biosynthesis - Mycobacterium</a> + </small> + </p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3797</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3797" target="_blank" + rel="noreferrer noopener">Rv3797</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O53577" + target="_blank" rel="noreferrer noopener">O53577</a> + </td> + <td>snp</td> + <td>synonymous_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..4251297&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..4251297" + target="_blank" rel="noreferrer noopener">4251297</a> + </td> + <td>C</td> + <td>G</td> + <td>protein_coding</td> + <td>c.213C>G</td> + <td>p.Gly71Gly</td> + <td>LOW</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3798</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3798" target="_blank" + rel="noreferrer noopener">Rv3798</a> + </td> + <td> + <p>NA</p> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..4254290&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..4254290" + target="_blank" rel="noreferrer noopener">4254290</a> + </td> + <td>T</td> + <td>G</td> + <td>protein_coding</td> + <td>c.1298T>G</td> + <td>p.Leu433Arg</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3799c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3799c" target="_blank" + rel="noreferrer noopener">Rv3799c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O53578" + target="_blank" rel="noreferrer noopener">O53578</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..4254478&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..4254478" + target="_blank" rel="noreferrer noopener">4254478</a> + </td> + <td>G</td> + <td>A</td> + <td>protein_coding</td> + <td>c.1471C>T</td> + <td>p.His491Tyr</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + <tr> + <td>Chromosome</td> + <td>Rv3801c</td> + <td> + <a href="https://explorer.sanbi.ac.za/gene?q=Rv3801c" target="_blank" + rel="noreferrer noopener">Rv3801c</a> + </td> + <td> + <a href="https://explorer.sanbi.ac.za/search?q=O53580" + target="_blank" rel="noreferrer noopener">O53580</a> + </td> + <td>snp</td> + <td>missense_variant</td> + <td> + <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..4261499&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..4261499" + target="_blank" rel="noreferrer noopener">4261499</a> + </td> + <td>A</td> + <td>G</td> + <td>protein_coding</td> + <td>c.1568T>C</td> + <td>p.Val523Ala</td> + <td>MODERATE</td> + <td> + <p>NA</p> + </td> + </tr> + </tbody> + <tfoot class="thead-light"> + <tr> + <th scope="col">CHR</th> + <th scope="col">GENE</th> + <th scope="col">LOCUS</th> + <th scope="col">PRODUCT</th> + <th scope="col">TYPE</th> + <th scope="col">EFFECT</th> + <th scope="col">POS</th> + <th scope="col">REF</th> + <th scope="col">ALT</th> + <th scope="col">BIOTYPE</th> + <th scope="col">NUCLEOTIDE</th> + <th scope="col">CONSEQUENCE</th> + <th scope="col">IMPACT</th> + <th scope="col">PATHWAY</th> + </tr> + </tfoot> + </table> +</div> +</main> +<div class="mt-5"> +</div> + <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" + 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src="https://cdn.datatables.net/buttons/1.5.2/js/buttons.colVis.min.js"></script> + <script type="text/javascript" language="javascript" class="init"> + $(function () { + var table = $('#vcfreport').DataTable({ + lengthChange: false, + buttons: [{ + extend: 'csv', + text: 'Download CSV', + filename: 'vcf_with_no_protein' + }] + }); + table.buttons().container().appendTo('#vcfreport_wrapper .col-md-6:eq(0)'); + }); + </script> + </div> +</body> + +</html> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_with_no_protein_report.txt Thu Mar 17 07:33:00 2022 +0000 @@ -0,0 +1,22 @@ +#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