#!/bin/sh
#$ -S /bin/sh
# qsub -e globalBedSort.log.txt -o globalBedSort.log.txt chipatlas/sh/globalBedSort.sh
# 全ての ChIP + Open chromatin の BED をソートする
: > globalBedSort.log.txt
rm -rf tmpDirForBedSort
mkdir -p tmpDirForBedSort/sh
mkdir -p tmpDirForBedSort/global1

# ChIP-seq の qsortBed
cat << 'DDD' > tmpDirForBedSort/sh/globalBedSort.chip.sh
#!/bin/sh
#$ -S /bin/sh
genome=$1
Qval=$2
echo chipatlas/results/$genome/Bed$Qval/Bed/*.$Qval.bed| xargs awk '{
  if (FNR == 1) {
    split(FILENAME, a, "/")
    split(a[6], b, ".")
    SRX = b[1]
  }
  print $1 "\t" $2 "\t" $3 "\t" SRX "\t" $5
}'| bin/qsortBed > tmpDirForBedSort/global1/$genome.$Qval.bed
DDD

# Bisulfite-seq の qsortBed
cat << 'DDD' > tmpDirForBedSort/sh/globalBedSort.bmap.sh
#!/bin/sh
#$ -S /bin/sh
genome=$1
echo chipatlas/results/$genome/bmap/*/Bed/*.bed| xargs awk '{
  if (FNR == 1) {
    split(FILENAME, a, "/")
    split(a[7], b, ".")
    SRX = b[1]
    mr = b[2]
  }
  print $1 "\t" $2 "\t" $3 "\t" SRX "\t" mr
}'| bin/qsortBed > tmpDirForBedSort/global1/$genome.bs.bed
DDD

# qsortBed の実行
for genome in `ls chipatlas/results`; do
  for Qval in 05 10 20; do
    qsub -e /dev/null -o /dev/null -N BedSort1 -pe def_slot 8 tmpDirForBedSort/sh/globalBedSort.chip.sh $genome $Qval
  done
  qsub -e /dev/null -o /dev/null -N BedSort1 -pe def_slot 8 tmpDirForBedSort/sh/globalBedSort.bmap.sh $genome
done
~/bin/wait4qsub BedSort1 # 1 min

exit