50 lines
2.1 KiB
R
50 lines
2.1 KiB
R
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species = scan(textConnection("anoGam1 apiMel2 braFlo1 caeJap1 caePb1 caePb2 caeRem2 caeRem3
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canFam1 canFam2 cb1 cb3 cbJul2002 ce1 ce10 ce11 ce2 ce4 ce6 ceMay2003 danRer1 danRer2 danRer3
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danRer4 dm1 dm2 dm3 dp2 dp3 droSim1 droYak1 droYak2 eboVir3 equCab1 equCab2 fr1 fr2 galGal2
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galGal3 gasAcu1 hg10 hg11 hg12 hg13 hg15 hg16 hg17 hg18 hg19 hg38 hg6 hg7 hg8 mm1 mm10 mm2
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mm3 mm4 mm5 mm6 mm7 mm8 mm9 monDom4 monDom5 panTro1 panTro2 ponAbe2 priPac1 rheMac2 rn1 rn2
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rn3 rn4 rn6 rnJan2003 rnJun2003 sacCer1 sacCer2 sacCer3 sc1 scApr2003 susScr2 taeGut1 tetNig1 tetNig2"), what = "character")
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cytoband_list = lapply(species, function(s) {
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url = paste("https://hgdownload.cse.ucsc.edu/goldenPath/", s, "/database/cytoBand.txt.gz", sep = "")
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oe = try({
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download.file(url, destfile = paste0(s, ".cytoBand.txt.gz"), quiet = TRUE)
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d <- read.table(paste0(s, ".cytoBand.txt.gz"), colClasses = c("character", "numeric", "numeric", "character", "character"), sep = "\t", stringsAsFactors = FALSE)
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})
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if(file.exists(paste0(s, ".cytoBand.txt.gz"))) {
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file.remove(paste0(s, ".cytoBand.txt.gz"))
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}
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if(inherits(oe, "try-error")) {
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return(NULL)
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} else {
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return(d)
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}
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})
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names(cytoband_list) = species
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l = sapply(cytoband_list, is.null)
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cytoband_list = cytoband_list[!l]
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saveRDS(cytoband_list, file = "~/project/circlize/inst/extdata/cytoband_list.rds")
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chrom_info_list = lapply(species, function(s) {
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url = paste("https://hgdownload.cse.ucsc.edu/goldenPath/", s, "/database/chromInfo.txt.gz", sep = "")
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oe = try({
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download.file(url, destfile = paste0(s, ".chromInfo.txt.gz"), quiet = TRUE)
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d <- read.table(paste0(s, ".chromInfo.txt.gz"), colClasses = c("character", "numeric"), sep = "\t", stringsAsFactors = FALSE)[1:2]
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})
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if(file.exists(paste0(s, ".chromInfo.txt.gz"))) {
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file.remove(paste0(s, ".chromInfo.txt.gz"))
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}
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if(inherits(oe, "try-error")) {
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return(NULL)
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} else {
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return(d)
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}
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})
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names(chrom_info_list) = species
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l = sapply(chrom_info_list, is.null)
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chrom_info_list = chrom_info_list[!l]
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saveRDS(chrom_info_list, file = "~/project/circlize/inst/extdata/chrom_info_list.rds")
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