cd /BLUES/eric/ONT/5hmc_DMR

bedtools map -a hg38_1kb.windows.bed -b Primed_5hmC_pileup_30x.bed.gz -c 11 -o mean > Primed_1kb_5hmC_30x.tsv
bedtools map -a hg38_1kb.windows.bed -b Naive_5hmC_pileup_30x.bed.gz  -c 11 -o mean > Naive_1kb_5hmC_30x.tsv
bedtools map -a hg38_1kb.windows.bed -b TSC_5hmC_pileup_30x.bed.gz    -c 11 -o mean > TSC_1kb_5hmC_30x.tsv

paste Primed_1kb_5hmC_30x.tsv Naive_1kb_5hmC_30x.tsv TSC_1kb_5hmC_30x.tsv | \
awk '
BEGIN{
    OFS="\t";
    print "chr","start","end","Primed_5hmC","Naive_5hmC","TSC_5hmC","Naive_minus_Primed","TSC_minus_Naive"
}
{
    p = ($4  == "." ? "NA" : $4/100)
    n = ($8  == "." ? "NA" : $8/100)
    t = ($12 == "." ? "NA" : $12/100)

    d_np = (p=="NA" || n=="NA") ? "NA" : n-p
    d_tn = (n=="NA" || t=="NA") ? "NA" : t-n

    print $1,$2,$3,p,n,t,d_np,d_tn
}' > 5hmC_1kb_window_matrix_30x.tsv

awk 'BEGIN{OFS="\t"} NR==1 || ($7!="NA" && ($7>=0.05 || $7<=-0.05))' \
5hmC_1kb_window_matrix_30x.tsv \
> DMR_1kb_5hmC_abs_Naive_vs_Primed_30x.tsv

awk 'BEGIN{OFS="\t"} NR==1 || ($8!="NA" && ($8>=0.05 || $8<=-0.05))' \
5hmC_1kb_window_matrix_30x.tsv \
> DMR_1kb_5hmC_abs_TSC_vs_Naive_30x.tsv