91 lines
2.3 KiB
R
91 lines
2.3 KiB
R
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#
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# R models I/O utilities
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#
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#
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# write start model
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#
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write.model.start <- function(frq, what) {
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dir.create("models", showWarnings=F)
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fil <- paste0("models/start.", what, ".frq")
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notify("writing start model:", fil)
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cat("# start model :", what, "\n", file=fil)
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for (x in names(frq))
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cat(x, frq[x]/sum(frq), frq[x], "\n", file=fil, append=T)
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invisible(fil)
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}
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#
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# write stop model
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#
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write.model.stop <- function(frq, what) {
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dir.create("models", showWarnings=F)
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fil <- paste0("models/stop.", what, ".frq")
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notify("writing stop model:", fil)
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cat("# stop model :", what, "(freq. ignored)\n", file=fil)
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for (x in names(frq))
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cat(x, frq[x]/sum(frq), frq[x], "\n", file=fil, append=T)
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invisible(fil)
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}
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#
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# write splice3 model
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# [FIXME] positions are hard-coded
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#
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write.model.splice3 <- function(cons, what) {
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dir.create("models", showWarnings=F)
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fil <- paste0("models/splice3.", what, ".frq")
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notify("writing splice3 model:", fil)
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.catcons <- function(i) {
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cat(round(cons[c("a","c","g","t"), i]*100, 0), "\n",
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file=fil, append=T)
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}
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cat("# 3' splice model :", what, "\n", file=fil)
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cat("# A C G T\n", file=fil, append=T)
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sapply(seq.int(1, 4), .catcons)
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cat("splice\n", file=fil, append=T)
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sapply(seq.int(6, 11), .catcons)
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invisible(fil)
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}
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#
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# write splice5 model
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# [FIXME] positions are hard-coded
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#
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write.model.splice5 <- function(cons, what) {
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dir.create("models", showWarnings=F)
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fil <- paste0("models/splice5.", what, ".frq")
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notify("writing splice5 model:", fil)
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.catcons <- function(i) {
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cat(round(cons[c("a","c","g","t"), i]*100, 0), "\n",
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file=fil, append=T)
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}
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cat("# 5' splice model :", what, "\n", file=fil)
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cat("# A C G T\n", file=fil, append=T)
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sapply(seq.int(13, 18), .catcons)
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cat("splice\n", file=fil, append=T)
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sapply(seq.int(20, 23), .catcons)
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invisible(fil)
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}
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#
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# write splice3/5 uniform model
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#
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write.unif.splice <- function(pos, what) {
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dir.create("models", showWarnings=F)
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fil <- paste0("models/splice", pos, ".", what, ".frq")
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notify("writing uniform splice", pos, "model:", fil)
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cat("# 3'/5' splice null model", file=fil)
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cat("# A C G T\n", file=fil, append=T)
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cat("25 25 25 25\n", file=fil, append=T)
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cat("splice\n", file=fil, append=T)
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cat("25 25 25 25\n", file=fil, append=T)
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invisible(fil)
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}
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