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| colorfun=function(feature) { | |
| if(feature.get('cosmic_attrs')) return 'red'; | |
| else if(feature.get('clinvar_attrs')) return 'cyan'; | |
| else if(feature.get('dbsnp_attrs')) return 'green'; | |
| else if(feature.get('snpeff_attrs')) return 'goldenrod'; | |
| else if(feature.get('snpeff_0_attrs')) return 'orange'; | |
| else if(feature.get('wellderly_attrs')) return 'purple'; | |
| else return 'lightgreen'; | |
| } | |
| cancerColor=function(feature) { | |
| if(feature.get('cosmic_attrs').tumor_site == 'colon') { return 'rgb(176,23,31)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'breast') { return 'rgb(0,0,200)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'kidney') { return 'rgb(255,65,0)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'prostate') { return 'rgb(255,182,193)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'large_intestine') { return 'rgb(139,69,69)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'urinary_tract') { return 'rgb(200,200,0)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'oesophagus') { return 'rgb(128,0,128)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'ovary') { return 'rgb(0,250,154)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'cervix') { return 'rgb(0,230,124)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'bone') { return 'rgb(100,100,80)'; } | |
| if(feature.get('cosmic_attrs').tumor_site == 'endometrium') { return 'rgb(129,59,59)'; } | |
| return 'rgb(128,128,128)'; | |
| } | |
| randomNumberLabel = function(track,feature,div) { | |
| return 'Label from a JS callback (random number: '+Math.random()+')'; | |
| } | |
| randomNumberTitle = function(track,feature,div) { | |
| return 'Title from a JS callback (random number: '+Math.random()+')'; | |
| } | |
| nameViaCallback = function(feature) { | |
| return feature.get('Name')+' (via JS callback)'; | |
| } | |
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| { | |
| "names" : { | |
| "type" : "MyVariantViewer/Store/Names/REST", | |
| "url" : "http://myvariant.info/v1/query" | |
| }, | |
| "tracks": [ | |
| { | |
| "label": "clinvar.0801.total", | |
| "urlTemplate": "../vcf/clinvar_20170801.vcf.gz", | |
| "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", | |
| "type": "CanvasVariants", | |
| "category": "Clinvar", | |
| }, | |
| { | |
| "style" : { | |
| "color" : "red" | |
| }, | |
| "label": "clinvar.0801.pathogenic", | |
| "urlTemplate": "../vcf/clinvar_20170801.pathogenic.vcf.gz", | |
| "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", | |
| "type": "CanvasVariants", | |
| "category": "Clinvar", | |
| }, | |
| { | |
| "chunkSize":20000, | |
| "storeClass":"JBrowse/Store/Sequence/StaticChunked", | |
| "urlTemplate":"seq/{refseq_dirpath}/{refseq}-", | |
| "category":"Reference sequence", | |
| "type":"SequenceTrack", | |
| "label":"DNA", | |
| "seqType":"dna", | |
| "key":"Reference sequence" | |
| }, | |
| { | |
| "hg19" : true, | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Genes_v3", | |
| "urlTemplate" : "https://mygene.info/v3/query?q=hg19.{refseq}:{start}-{end}&fields=all&size=1000", | |
| "subParts" : [ | |
| "exon" | |
| ], | |
| "category": "MyGene.info", | |
| "type" : "MyVariantViewer/View/Track/CanvasFeatures", | |
| "label" : "MyGene.info v3" | |
| }, | |
| { | |
| "hg19" : true, | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Genes", | |
| "urlTemplate" : "https://mygene.info/v2/query?q=hg19.{refseq}:{start}-{end}&fields=all&size=1000", | |
| "subParts" : [ | |
| "exon" | |
| ], | |
| "category": "MyGene.info", | |
| "type" : "MyVariantViewer/View/Track/CanvasFeatures", | |
| "label" : "MyGene.info v2" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "{colorfun}", | |
| "featureScale" : 0.5 | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end}&size=1000&email=colin.diesh@gmail.com", | |
| "type" : "CanvasFeatures", | |
| "category": "MyVariant.info", | |
| "label" : "MyVariant.info", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#665" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:evs&size=1000&email=colin.diesh@gmail.com&fields=evs", | |
| "type" : "CanvasFeatures", | |
| "category": "MyVariant.info", | |
| "label" : "MyVariant.info evs", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "magenta" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:gwassnps&size=1000&email=colin.diesh@gmail.com&fields=gwassnps", | |
| "category": "MyVariant.info", | |
| "type" : "CanvasFeatures", | |
| "optimizer": true, | |
| "label" : "MyVariant.info gwassnps", | |
| "key": "MyVariant.info gwas catalog", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#aae" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:cosmic&size=1000&email=colin.diesh@gmail.com&fields=cosmic", | |
| "type" : "CanvasFeatures", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "label" : "MyVariant.info cosmic", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#5fa" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:mutdb&size=1000&email=colin.diesh@gmail.com&fields=mutdb", | |
| "optimizer": true, | |
| "category": "MyVariant.info", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info mutdb", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#119" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:snpeff&size=1000&email=colin.diesh@gmail.com&fields=snpeff", | |
| "category": "MyVariant.info", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info snpeff", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#a84" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:emv&size=1000&email=colin.diesh@gmail.com&fields=emv", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info emvclass", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#3f9" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:docm&size=1000&email=colin.diesh@gmail.com&fields=docm", | |
| "category": "MyVariant.info", | |
| "type" : "CanvasFeatures", | |
| "optimizer": true, | |
| "label" : "MyVariant.info docm", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#b44" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:snpedia&size=1000&email=colin.diesh@gmail.com&fields=snpedia", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info snpedia", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "cyan" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:clinvar&size=1000&email=colin.diesh@gmail.com&fields=clinvar", | |
| "optimizer": true, | |
| "type" : "CanvasFeatures", | |
| "category": "MyVariant.info", | |
| "label" : "MyVariant.info clinvar", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style": { | |
| "color" : "#4a9" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:cadd&size=1000&email=colin.diesh@gmail.com&fields=cadd", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info cadd", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#22a" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:grasp&size=1000&email=colin.diesh@gmail.com&fields=grasp", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info grasp", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#b33" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:exac&size=1000&email=colin.diesh@gmail.com&fields=exac", | |
| "type" : "CanvasFeatures", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "label" : "MyVariant.info exac", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#b3b" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:wellderly&size=1000&email=colin.diesh@gmail.com&fields=wellderly", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info wellderly", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#5e4" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:dbsnp&size=1000&email=colin.diesh@gmail.com&fields=dbsnp", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info dbsnp", | |
| "category": "MyVariant.info", | |
| "optimizer": true, | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond" | |
| }, | |
| { | |
| "style" : { | |
| "color" : "#742" | |
| }, | |
| "baseUrl" : "https://myvariant.info/v1/", | |
| "storeClass" : "MyVariantViewer/Store/SeqFeature/Variants", | |
| "category": "MyVariant.info", | |
| "urlTemplate" : "query?q={refseq}:{start}-{end} AND _exists_:dbnsfp&size=1000&email=colin.diesh@gmail.com&fields=dbnsfp", | |
| "type" : "CanvasFeatures", | |
| "label" : "MyVariant.info dbnsfp", | |
| "glyph" : "MyVariantViewer/View/FeatureGlyph/Diamond", | |
| "optimizer": true | |
| } | |
| ], | |
| "formatVersion":1, | |
| "plugins": [ | |
| "MyVariantViewer", | |
| "HideTrackLabels", | |
| "NeatHTMLFeatures", | |
| "NeatCanvasFeatures", | |
| "RegexSequenceSearch", | |
| "SVGLollipopTrack" | |
| ], | |
| "include": ["functions.conf"], | |
| "highResolutionMode":2, | |
| "classicMenu": true, | |
| } |
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| dataset_id=hg19 | |
| [datasets.hg19] | |
| name = hg19 |
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