gistfile1.txt

#!/bin/bash
#
# /stornext/snfs1/next-gen/drio-scratch/bfast_related/dnaa/dqc postalignqc -f 
# -f /stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa
# -r 0:2000 /Users/drio/projects/synthetic.pipe/bf.bwt.sorted.bam > /tmp/foo.txt 
# R CMD BATCH '--args in.file="/tmp/foo.txt" out.type="png" space="0" expid="test"' plot_dqc_postalignqc.R 
#
sample="test"
data_f="/tmp/data.txt"
gp_cfg_f="/tmp/gplot.${sample}.cfg"
n_cycles="50"

input_file=$1

#1       220     5220
#2       252     5215
cat $input_file | head -52 | tail -${n_cycles} |\
awk '{print $1"\t"$4"\t"$5}' > $data_f

(
cat <<-EOF
set terminal png nocrop size 750,450
set nokey
set xtics 2
set grid x y
#set datafile separator ","
set t png
#set xrange [0:800]
#set yrange [0:100]
set output "output.png"
set xlabel "cycle"
set ylabel "mismatch rate"
set title "$sample"
plot "$data_f" using 1:((\$2*100)/\$3)
EOF
) > $gp_cfg_f

cat $gp_cfg_f | gnuplot