mummer2ggplot

#!/bin/bash

set -e

pushd `dirname $0` > /dev/null
SCRIPTPATH=`pwd`
popd > /dev/null

if [[ $# -lt 2 ]]; then
    echo "usage: mummer2ggplot inputprefix outputdir"
    exit 1
fi

inputprefix=$1
outputdir=$2

# make coords
cat ${inputprefix}.[fr]plot \
    | awk '/^[1-9]/' \
    | awk '
NR%2==1 {a=$1;b=$2} 
NR%2==0 {if($2>b) {
            print a,b,$1,$2,$3,"+"
        }else{
            print a,b,$1,$2,$3,"-"
        }}' \
    | sort -n \
           > ${inputprefix}.ggplot

# make ticks
sed ':a;N;$!ba;s/\\\n//g' ${inputprefix}.gp \
    | awk '/^set ytics/' \
    | sed 's/set ytics (  //' \
    | sed 's/ )//' \
    | sed 's/,  /\n/g' \
    | sed 's/ /,/' \
    | awk '{gsub(/"/, "", $1); print $1,$2;}' \
          > ${inputprefix}.yticks

sed ':a;N;$!ba;s/\\\n//g' ${inputprefix}.gp \
    | awk '/^set xtics/' \
    | sed 's/set xtics rotate (  //' \
    | sed 's/ )//' \
    | sed 's/,  /\n/g' \
    | sed 's/ /,/' \
    | awk '{gsub(/"/, "", $1); print $1,$2;}' \
          > ${inputprefix}.xticks

Rscript ${SCRIPTPATH}/mummerplot.R ${outputdir}/$(basename ${inputprefix}) \
        ${inputprefix}.ggplot ${inputprefix}.xticks ${inputprefix}.yticks