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Included hg38 to create IGV json session file #1

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Included hg38 to create IGV json session file #1

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43 changes: 39 additions & 4 deletions scripts/R/make_igv_json.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,12 @@ out_path <- "test.json"
out_path <- args[2]

# Specify reference genome.
genome <- "hg19"
genome <- "hg38"

genome <- args[3]
genome <- as.character(genome)

supported_genomes <- c("hg19", "mm10")
supported_genomes <- c("hg19", "mm10", "hg38")

genome_pass <- genome %in% supported_genomes

Expand Down Expand Up @@ -50,13 +50,13 @@ mdat <- mdat[mdat$Include_in_browser, ]
mdat <- mdat[!is.na(mdat$url), ]

message("##############")
message("Creating hg19 IGV session file...")
message("Creating IGV session file...")
message("##############")

# setup for human hg19
hg19_seed <- c('{"reference": {
"id": "hg19",
"name": "Human (CRCh37/hg19)",
"name": "Human (GRCh37/hg19)",
"fastaURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",
"indexURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai",
"cytobandURL": "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
Expand Down Expand Up @@ -112,6 +112,39 @@ mm10_seed <- c('{
]
}')

# setup for human hg38
hg38_seed <- c('{
"version": "2.12.6",
"showSampleNames": false,
"reference": {
"id": "hg38",
"name": "Human (GRCh38/hg38)",
"fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
"indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",
"chromosomeOrder": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"
},
"tracks": [
{
"type": "sequence",
"order": -9007199254740991
},
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.txt.gz.tbi",
"visibilityWindow": -1,
"supportsWholeGenome": false,
"removable": false,
"order": 1000000,
"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$",
"type": "annotation"
}
]
}')


# Set json seed based on argument 2

Expand All @@ -121,6 +154,8 @@ if (genome == "hg19"){
seed <- hg19_seed
} else if (genome == "mm10"){
seed <- mm10_seed
} else if (genome == "hg38"){
seed <- hg38_seed
}


Expand Down