#!/bin/bash
#
# script to pull bigWig summary for housekeeper genes

# bigWigSummary CA1_CB.neg.bw chr6 125161715 125166467 dataPoints=1
# AUC=$(bigWigSummary CA1_CB.neg.bw chr6 125161715 125166467 1)

# grep "Gapdh$\|Actb$\|Ppib\|Rpl22$" gencode.vM12.genes.txt
#
# chr6   HAVANA   gene   125161715   125166467   .   -   .   protein_coding   Gapdh

export TAB=$(echo -e '\011');

HKS="Gapdh Actb Tubb2a Pgk1 Eif4g2 Eif4g3 Pten Smarca2";
#BWS=$(ls *.bw);
BWSTEMS=$(ls *bw | perl -p -e 's/[.](pos|neg).*//;' | uniq);

for HK in ${HKS}; do
   for BWSTEM in ${BWSTEMS}; do
      GLINE=($(grep "${HK}$" gencode.vM12.genes.txt));
      if [ "-" == "${GLINE[6]}" ]; then
         BW="${BWSTEM}.neg.bw";
      else
         BW="${BWSTEM}.pos.bw";
      fi;
      #echo -e "${FYELLOW}bigWigSummary ${BW} ${GLINE[0]} ${GLINE[3]} ${GLINE[4]} 1${RESET}";
      AUC=$(bigWigSummary ${BW} ${GLINE[0]} ${GLINE[3]} ${GLINE[4]} 1);
      echo "${BW}${TAB}${HK}${TAB}${AUC}";
   done;
done;