Mercurial > repos > kyost > atac_primer_tool
view make_window_bed.R @ 2:6f5ce4e865a5 draft
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author | kyost |
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date | Sat, 28 Apr 2018 19:45:57 -0400 |
parents | fd3ea97a96bc |
children | 72571a30f17b |
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## Command to run tool: # Rscript --vanilla make_window_bed.R qPCR_peaks.bed window_size output_file # Set up R error handling to go to stderr options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) # Avoid crashing Galaxy with an UTF8 error on German LC settings loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") args <- commandArgs(TRUE) qPCR_bed <- args[1] window_size <- strtoi(args[2]) output_file <- args[3] qPCR_table <- read.delim(qPCR_bed, header=FALSE, stringsAsFactors=FALSE) make_windows_bed <- function(a, size) { #a is a bed file containing peaks of interest and coordinates #generates bed file with overlapping windows spanning each peak of specified size return_bed <- data.frame() for (i in 1:nrow(a)) { line <- data.frame(a[i,],stringsAsFactors=FALSE) peak_name <- as.character(line[1,4]) line <- rbind(line , data.frame(V1=as.character(line[1,1]) , V2=line[1,2] , V3=line[1,2]+size , V4=as.character(paste(as.character(line[1,4]) , "_window1" , sep = "") ) ) ) count <- as.numeric(line[1,2])+size nline <- 2 while (count < as.numeric(line[1,3])) { line <- rbind(line , data.frame(V1=as.character(line[nline,1]) , V2=line[nline,2]+floor(size/4) , V3=line[nline,2]+floor(size/4)+size , V4=as.character(paste(as.character(line[1,4]) , "_window" , as.character(nline) , sep = "") ) ) ) nline <- nline + 1 count <- as.numeric(line[nline,3]) } return_bed <- rbind(return_bed,line) } return(return_bed) } output <- make_windows_bed(qPCR_table, window_size) write.table(output , output_file , sep = "\t" , col.names = FALSE , row.names = FALSE , quote = FALSE)