Re: [Gmod-ajax] JBrowse hg19 Demo

[Mitch S. <mit...@be...>]

bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ChromosomeBand.bed --tracklabel ChromosomeBand --key "Chromosome Band" --cssClass exon --getLabel --autoComplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CpGIslands.bed --tracklabel CpGIslands --key "CpG Islands" --cssClass basic --clientConfig '{"featureCss": "background-color: #0D0; height: 8px", "histCss": "background-color: #3D3"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Gap.bed --tracklabel Gap --key "Gap" --cssClass --cssClass basic --clientConfig '{"featureCss": "background-color: #777; height: 8px", "histCss": "background-color: #777"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-daught-2878.bed --tracklabel "GenomeVariants-CEU-daught-2878" --key "GenomeVariants - CEU daught '2878" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/bacEndPairs.bed --tracklabel bacEndPairs --key "BAC End Pairs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/EnsemblGenes.bed --tracklabel EnsemblGenes --key "Ensembl Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-mother-2892.bed --tracklabel "GenomeVariants-CEU-mother-2892" --key "GenomeVariants - CEU mother '2892" --cssClass basic --clientConfig '{"featureCss": "background-color: #AF6; height: 8px", "histCss": "background-color: #BF8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Venter.bed --tracklabel "GenomeVariants-Venter" --key "GenomeVariants - Venter" --cssClass basic --clientConfig '{"featureCss": "background-color: #FF00AF; height: 8px", "histCss": "background-color: #FF66CF"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Watson.bed --tracklabel "GenomeVariants-Watson" --key "GenomeVariants - Watson" --cssClass basic --clientConfig '{"featureCss": "background-color: #1834BA; height: 8px", "histCss": "background-color: #576DD9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Yh1.bed --tracklabel "GenomeVariants-Yh1" --key "GenomeVariants - Yh1" --cssClass basic --clientConfig '{"featureCss": "background-color: #3D59CC; height: 8px", "histCss": "background-color: #5E79E6"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GWASCatalog.bed --tracklabel "GWASCatalog" --key "GWAS Catalog" --cssClass basic --clientConfig '{"featureCss": "background-color: #00F; height: 8px", "histCss": "background-color: #88F"}' --getLabel --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/HumanmRNAs-all_mrna.bed --tracklabel all_mrna --key "Human mRNAs" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --autoComplete label --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MGCGenes.bed --tracklabel "MGCGenes" --key "MGC Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/N-SCAN.bed --tracklabel "N-SCAN" --key "N-SCAN" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/RefSeqGenes.bed --tracklabel "RefSeqGenes" --key "RefSeq Genes" --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead --getLabel --getSubs --autocomplete label
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/STSMarkers.bed --tracklabel STSMarkers --key "STS Markers" --cssClass exon
history | grep flatfile-to-json | grep hg19-bed > ~/ff2json.txt
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/Exoniphy.bed --tracklabel Exoniphy --key "Exoniphy" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/CCDS.bed --tracklabel CCDS --key "Consensus CDS" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getLabel --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-CEU-father-2891.bed --tracklabel "GenomeVariants-CEU-father-2891" --key "GenomeVariants - CEU father '2891" --cssClass basic --clientConfig '{"featureCss": "background-color: #6F6; height: 8px", "histCss": "background-color: #8F8"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-Sjk.bed --tracklabel "GenomeVariants-Sjk" --key "GenomeVariants - Sjk" --cssClass basic --clientConfig '{"featureCss": "background-color: #BA9843; height: 8px", "histCss": "background-color: #D4B56A"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/InterruptedRpts.bed --tracklabel InterruptedRpts --key "Interrupted Rpts" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/MapContigs.bed --tracklabel MapContigs --key "Map Contigs" --cssClass exon
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/OMIMGenes.bed --tracklabel OMIMGenes --key "OMIM Genes" --cssClass feature
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/ORFeomeClones.bed --tracklabel ORFeomeClones --key "ORFeome Clones" --cssClass generic_parent --subfeatureClasses '{"CDS": "generic_part_a"}' --getSubs
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SegmentalDups.bed --tracklabel SegmentalDups --key "Segmental Dups" --cssClass feature5
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SimpleRepeats.bed --tracklabel SimpleRepeats --key "Simple Repeats" --cssClass feature3
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/GenomeVariants-YRI-daught-9240.bed --tracklabel "GenomeVariants-YRI-daught-9240" --key "GenomeVariants - YRI daught '9240" --cssClass basic --clientConfig '{"featureCss": "background-color: #7245BB; height: 8px", "histCss": "background-color: #8F62D9"}'
bin/flatfile-to-json.pl --bed ~/data/ucsc/hg19-bed/SplicedESTs.bed --tracklabel SplicedESTs --key "Spliced ESTs" --cssClass generic_parent --subfeatureClasses '{"CDS": "match_part"}' --getSubs