compute average scores for share intervals

go.sh

cat a.bed
chr1	10	50	10

cat b.bed
chr1	20	40	20

cat c.bed
chr1	30	33	30

# Find the sub-intervals shared and unique to each file.
bedtools multiinter -i a.bed b.bed c.bed | column -t
chr1  10  20  1  1      1  0  0
chr1  20  30  2  1,2    1  1  0
chr1  30  33  3  1,2,3  1  1  1
chr1  33  40  2  1,2    1  1  0
chr1  40  50  1  1      1  0  0

# Intersect the sub-intervals with the original intervals to collect the scores
bedtools multiinter -i a.bed b.bed c.bed \
    | bedtools intersect -a - -b a.bed b.bed c.bed -wa -wb \
    | column -t
chr1  10  20  1  1      1  0  0  1  chr1  10  50  10
chr1  20  30  2  1,2    1  1  0  1  chr1  10  50  10
chr1  20  30  2  1,2    1  1  0  2  chr1  20  40  20
chr1  30  33  3  1,2,3  1  1  1  1  chr1  10  50  10
chr1  30  33  3  1,2,3  1  1  1  2  chr1  20  40  20
chr1  30  33  3  1,2,3  1  1  1  3  chr1  30  33  30
chr1  33  40  2  1,2    1  1  0  1  chr1  10  50  10
chr1  33  40  2  1,2    1  1  0  2  chr1  20  40  20
chr1  40  50  1  1      1  0  0  1  chr1  10  50  10


# Grooupby the sub-intervals with the mean score from each of the original files.
bedtools multiinter -i a.bed b.bed c.bed \
    | bedtools intersect -a - -b a.bed b.bed c.bed -wa -wb \
    | bedtools groupby -g 1-5 -c 13 -o mean \
    | column -t
chr1  10  20  1  1      10
chr1  20  30  2  1,2    15
chr1  30  33  3  1,2,3  20
chr1  33  40  2  1,2    15
chr1  40  50  1  1      10