mfoll

#! /usr/bin/env Rscript
data=read.table(pipe("bjobs -u all -w | grep RUN | awk '{print $2\" \"$6}'"),stringsAsFactors = F,col.names = c("username","cpus"))
data[,2]=gsub("^cn.+$",1,data[,2])
data[,2]=as.numeric(gsub("^(.+)\\*cn.+$","\\1",data[,2]))
res=aggregate(cpus ~ username, data, sum)
print(res[order(res$cpus,decreasing = T),],row.names = FALSE)

mfoll

#! /usr/bin/env Rscript

# With no argument provided, produce a graph since the begining of the year
# Argument can be "2016/03/01,2016/12/31" or "2016/03/01,"

if (!is.na(commandArgs(TRUE)[1])) {
	time_string=commandArgs(TRUE)[1]
} else {
	time_string=paste(format(Sys.time(), "%Y"),"/01/01,",sep="")
}

mfoll

BEGIN {
  OFS = "\t"; # tab-delimited output
}
# Use substr instead of regex to match a starting ">"
substr($0, 1, 1) == ">" {
  if (seqlen) {
    # Only print info for this sequence if no target was given
    # or its id matches the target.
    if (! target || id == target) {
      print id, seqlen;

mfoll

get_info=function(info,field,num=T) {
  get_single_info=function(single_info,field) { 
    grep_res=grep(paste("^",field,"=",sep=""),unlist(strsplit(single_info,";")),value=T)
    if (length(grep_res)>0) strsplit(grep_res,"=")[[1]][2] else NA
  }
  res=unlist(lapply(info,get_single_info,field))
  if (num) as.numeric(res) else res
}

get_genotype=function(genotype,format,field,num=T) {

mfoll

qq = function(pvector, title="Quantile-quantile plot of p-values",red=NULL) {
  # adapted from http://www.gettinggeneticsdone.com/2009/11/qq-plots-of-p-values-in-r-using-ggplot2.html
  pvector[pvector==0]=min(pvector[pvector>0])
  obs <- -log10(pvector)
  N <- length(obs) ## number of p-values
  null <- -log(1:N/N,10)
  MAX <- max(c(obs,null))
  c95 <- rep(0,N)
  c05 <- rep(0,N)
  for(i in 1:N){