downloadSuperFreqDbSNP = function(directory='superFreqDbSNP', genome='hg19') {
if ( genome == 'hg19' ) {
if ( !dir.exists(directory) ) {
cat('Creating superFreq dbSNP annotation directory ', directory, '.\n')
dir.create(directory)
}
#hg19 dbSNP
url = paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/dbSNP/dbAFnew.Rdata')
figshareUrl = 'https://figshare.com/ndownloader/files/31278718'
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
#hg19 ExAC
url = paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/dbSNP/exac.Rdata')
figshareUrl = 'https://figshare.com/ndownloader/files/31278721'
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
}
else if ( genome == 'hg38' ) {
if ( !dir.exists(directory) ) {
cat('Creating superFreq dbSNP annotation directory ', directory, '.\n')
dir.create(directory)
}
directory = paste0(directory, '/hg38')
if ( !dir.exists(directory) ) {
cat('Creating superFreq dbSNP annotation subdirectory ', directory, '.\n')
dir.create(directory)
}
#hg38 dbSNP
url = paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/dbSNP/hg38/dbAFnew.Rdata')
figshareUrl = 'https://figshare.com/ndownloader/files/31278724'
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
#hg19 ExAC
url = paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/dbSNP/hg38/exac.Rdata')
figshareUrl = 'https://figshare.com/ndownloader/files/31278727'
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
}
else if ( genome == 'mm10' ) {
if ( !dir.exists(directory) ) {
cat('Creating superFreq dbSNP annotation directory ', directory, '.\n')
dir.create(directory)
}
directory = paste0(directory, '/mm10')
if ( !dir.exists(directory) ) {
cat('Creating superFreq dbSNP annotation subdirectory ', directory, '.\n')
dir.create(directory)
}
#mm10 dbSNP
url = paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/dbSNP/mm10/dbAFnew.Rdata')
figshareUrl = 'https://figshare.com/ndownloader/files/31278730'
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
}
else stop('Genome ', genome, ' not supported for dbSNP in superFreq, sorry.')
}
downloadSuperFreqCOSMIC = function(directory='superFreqCOSMIC', genome='hg19') {
if ( !dir.exists(directory) ) {
cat('Downloading superFreq COSMIC annotation to', directory, '.\n')
dir.create(directory)
}
urls =
paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/',
c('COSMIC/allCosmicCounts_hg19.Rdata', 'COSMIC/cosmicCounts.Rdata', 'ClinVar/clinvar19.Rdata'))
filenames = basename(urls)
figshareUrls = c('https://figshare.com/ndownloader/files/31278697',
'https://figshare.com/ndownloader/files/31278712',
'https://figshare.com/ndownloader/files/31278706')
if ( genome == 'hg38' ) {
urls =
paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/',
c('COSMIC/allCosmicCounts_hg38.Rdata', 'COSMIC/cosmicCounts.Rdata', 'ClinVar/clinvar38.Rdata'))
filenames = basename(urls)
figshareUrls = c('https://figshare.com/ndownloader/files/31278700',
'https://figshare.com/ndownloader/files/31278712',
'https://figshare.com/ndownloader/files/31278709')
}
if ( genome == 'mm10' ) {
urls =
c('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/COSMIC/CCGD_export.csv',
'https://figshare.com/ndownloader/files/36269079')
filenames = c('CCGD_export.csv', 'MGIBatchReport_20220629_032731_filtered.txt')
figshareUrls = c('https://figshare.com/ndownloader/files/31278703',
'https://figshare.com/ndownloader/files/36269079')
}
for ( i in 1:length(figshareUrls) ) {
url = figshareUrls[i]
destFile = paste0(directory, '/', filenames[i])
if ( !file.exists(destFile) ) superFreq:::downloadFile(url, destfile = destFile)
}
}
#change how this is called to download to superFreq resources rather than to the R directory.
downloadCaptureRegions = function(directory, genome='hg19', mode='exome', binSize=10000) {
url = ''
if ( genome == 'hg19' & mode %in% c('exome', 'RNA') ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/hg19exons.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278643',
'https://figshare.com/ndownloader/files/31278646',
'https://figshare.com/ndownloader/files/31278649')
}
if ( genome == 'hg38' & mode %in% c('exome', 'RNA') ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/hg38exons.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278661',
'https://figshare.com/ndownloader/files/31278664',
'https://figshare.com/ndownloader/files/31278667')
}
if ( genome == 'mm10' & mode %in% c('exome', 'RNA') ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/mm10exons.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278679',
'https://figshare.com/ndownloader/files/31278682',
'https://figshare.com/ndownloader/files/31278685')
}
if ( genome == 'hg19' & mode == 'genome' & binSize == 10000 ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/hg19genome.10k.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278652',
'https://figshare.com/ndownloader/files/31278655',
'https://figshare.com/ndownloader/files/31278658')
}
if ( genome == 'hg38' & mode == 'genome' & binSize == 10000 ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/hg38genome.10k.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278670',
'https://figshare.com/ndownloader/files/31278673',
'https://figshare.com/ndownloader/files/31278676')
}
if ( genome == 'mm10' & mode == 'genome' & binSize == 10000 ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/captureRegions/mm10genome.10k.bed'
figshareUrls = c('https://figshare.com/ndownloader/files/31278688',
'https://figshare.com/ndownloader/files/31278691',
'https://figshare.com/ndownloader/files/31278694')
}
if ( url == '' ) {
catLog('\nERROR: Couldnt find any capture regions for genome ', genome, ' in mode ', mode, ' with binSize ', binSize, '\n\n')
stop('Couldnt find any capture regions for genome ', genome, ' in mode ', mode, ' with binSize ', binSize)
}
urls = c(url, gsub('.bed$', '.named.bed', url), gsub('.bed$', '.named.dn.bed', url))
for ( i in 1:3 ) {
url = urls[i]
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrls[i], destfile = destFile)
}
return(paste0(directory, '/', basename(urls[1])))
}
downloadSuperFreqAnnotation = function(directory='superFreqAnnotation', genome='hg19') {
if ( !dir.exists(directory) ) {
cat('Downloading superFreq annotation to', directory, '.\n')
dir.create(directory)
}
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/annotation/dumpHg19.Rdata'
figshareUrl = 'https://figshare.com/ndownloader/files/31278631'
if ( genome == 'hg38' ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/annotation/dumpHg38.Rdata'
figshareUrl = 'https://figshare.com/ndownloader/files/31278634'
}
if ( genome == 'mm10' ) {
url = 'http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/annotation/dumpMm10.Rdata'
figshareUrl = 'https://figshare.com/ndownloader/files/31278637'
}
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrl, destfile = destFile)
}
downloadSuperFreqSignatures = function(directory='superFreqSignatures') {
if ( !dir.exists(directory) ) {
cat('Downloading superFreq signatures to', directory, '.\n')
dir.create(directory)
}
urls =
paste0('http://gitlab.wehi.edu.au/flensburg.c/superFreq/raw/master/',
c('signatures/extendedPatternMx.Rdata', 'signatures/cosmicSignatures_v2_104.Rdata',
'signatures/mutagenSignatures.Rdata'))
figshareUrls = c('https://figshare.com/ndownloader/files/31278736',
'https://figshare.com/ndownloader/files/31278733',
'https://figshare.com/ndownloader/files/31278739')
for ( i in 1:3 ) {
url = urls[i]
destFile = paste0(directory, '/', basename(url))
if ( !file.exists(destFile) ) downloadFile(figshareUrls[i], destfile = destFile)
}
}
downloadFile = function(url, destfile) {
system(paste0('wget --no-check-certificate -O ', destfile, ' ', url))
}
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