converts chromosome names from Tair10 from ngsplot to numeric names

chr2num.R

#!/usr/bin/env Rscript

#copy .metainfo and .chrnames.endsembl from orig tar.gz in subfolder and change
# chrnames, ID
#tar with tar -zcvf Tair10numeric.tar.gz Tair10numeric


convertRdata <- function(){
  id <- "Tair10numeric"
  dir.create(id, recursive=TRUE, show=FALSE )
  dts <- dir(".", ".RData", full=TRUE)
  for(d in dts){
    print(d)
    tableName <- load(d)
    if(length(tableName) != 1){
       stop("object has unexpected name or multiple tables loaded ", tableName)
    }
    df <- get(tableName)
    df$chrom <- gsub("chr", "", df$chrom)
    bn <- basename(d)
    dt <- sub(".+?(\\..*)", "\\1", d)
    iddt <- paste(id, dt, sep="")
    outp <- paste(id,"/", iddt, sep="")
    print(tableName)
    print(length(df))
    save(df, list=tableName, file=outp)
  }
}

convertRdata()