for treatment in ${treatments[@]}; do
mkdir ${newPath}/${treatment}/GO_D0.v.D8/
mkdir ${newPath}/${treatment}/GO_D8.v.D16/
mkdir ${newPath}/${treatment}/GO_D0.v.D16/
awk -F'\t' 'BEGIN {OFS=FS} {log_fold_change=log(($10 + 0.1) / ($9 + 0.1)); $11=log_fold_change; print}' ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_temp.txt > ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog.txt
sort -r -n -k 11 ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog.txt > ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog_sorted.txt
cut -f1,2,3,4,5,6,7,8,9,10 ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog_sorted.txt > ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog_sorted_normal.txt
head -n 1000 ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_templog_sorted_normal.txt > ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_top1k.txt
awk -F'\t' 'BEGIN {OFS=FS} {log_fold_change=log(($10 + 0.1) / ($9 + 0.1)); $11=log_fold_change; print}' ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_temp.txt > ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog.txt
sort -r -n -k 11 ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog.txt > ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog_sorted.txt
cut -f1,2,3,4,5,6,7,8,9,10 ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog_sorted.txt > ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog_sorted_normal.txt
head -n 1000 ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_templog_sorted_normal.txt > ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_top1k.txt
awk -F'\t' 'BEGIN {OFS=FS} {log_fold_change=log(($10 + 0.1) / ($9 + 0.1)); $11=log_fold_change; print}' ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_temp.txt > ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog.txt
sort -r -n -k 11 ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog.txt > ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog_sorted.txt
cut -f1,2,3,4,5,6,7,8,9,10 ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog_sorted.txt > ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog_sorted_normal.txt
head -n 1000 ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_templog_sorted_normal.txt > ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_top1k.txt
findGO.pl ${newPath}/${treatment}/D0_${treatment}.v.D8_${treatment}_top1k.txt human ${newPath}/${treatment}/GO_D0.v.D8/
findGO.pl ${newPath}/${treatment}/D8_${treatment}.v.D16_${treatment}_top1k.txt human ${newPath}/${treatment}/GO_D8.v.D16/
findGO.pl ${newPath}/${treatment}/D0_${treatment}.v.D16_${treatment}_top1k.txt human ${newPath}/${treatment}/GO_D0.v.D16/
done;