ibowankenobi-i-pv/sample-configs/configWithAbsolutePaths.json

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

{
	"path": "absolute",
	"proteinFileName": "D:\\path\\to\\your/fasta.txt",
	"mrnaFileName": "D:\\path\\to\\your/mRNA.txt",
	"conservation":{
		"consFileName": "D:\\path\\to\\your/conservation.txt",
		"barHeight": 0,
		"defVal": "Hmm"
	},
	"name": "NFKB",
	"domains": [
		{
			"start": 50,
			"end": 126,
			"name": "domain_X",
			"color": "vdred"
		},
		{
			"start": 350,
			"end": 460,
			"name": "domain_Y",
			"color": "lblue"
		}
	],
	"variation":{
		"format": "ensembl",
		"fileName": "D:\\path\\to\\your/mart_export.txt",
		"skipHeader": 1,
		"separator": "tab",
		"colBaseChange": 4,
		"colSubsType": 4,
		"colSubsCoords": 8,
		"colValStat": 4,
		"colBaseChangeStrand": 3,
		"colGeneStrand": "+",
		"transcriptID": "ENST00000505458",
		"colTranscriptID": 6,
		"colPolyphen2": 10,
		"colSift2": 11,
		"maf": 5
	},
	"markups": [
		{
			"start": 60,
			"end": 125,
			"name": "some_region",
			"prop": "prop_x",
			"color": "magenta"
		}
	],
	"circos": {
		"run": 1,
		"path": "",
		"output": "D:\\path\\to\\your\\custom\\output\\folder",
		"mkdir": 1
	},
	"datatracks": {
		"cleanup": 1,
		"mkdir": 1,
		"copy": "D:\\path\\to\\your\\custom\\datatracks\\folder",
		"move": "D:\\path\\to\\your\\custom\\datatracks\\folder"
	}
}