Data sets give at the end.
LOAD, PRINT, COUNT
a = LOAD "tiny_a.bed";
PRINT a;
c=COUNT a;
PRINT c;
Result
chr1 1 4 a1 1 +
chr1 6 8 a2 2 +
chr1 14 17 a3 3 +
chr1 500 501 a4 4 +
chr2 500 501 a4 4 +
5
Unary INTERSECT
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
c = LOAD "../data/tiny_c.bed";
d = LOAD "../data/tiny_d.bed";
e = INTERSECT a,b,c,d;
PRINT e;
f=COUNT e;
PRINT f;
Result chr1 14 17 a3 3 + chr1 12 16 b3 3 + chr1 15 18 c3 + chr1 15 18 d3 3 + 1
Mutlti-file LOAD, Binary INTERSECT
a = LOAD "tiny_a.bed";
b = LOAD "tiny_b.bed";
c = LOAD "tiny_*.bed";
e = a,b INTERSECT c;
PRINT e;
f = COUNT e;
PRINT f;
Result
a::tiny_a.bed
chr1 1 4 a1 1 + chr1 1 4 a1 1 + 3
chr1 6 8 a2 2 + chr1 6 8 a2 2 + 2
chr1 14 17 a3 3 + chr1 14 17 a3 3 + 3
chr1 500 501 a4 4 + chr1 500 501 a4 4 + 1
chr2 500 501 a4 4 + chr2 500 501 a4 4 + 1
a::tiny_b.bed
chr1 1 4 a1 1 + chr1 3 7 b1 1 - 1
chr1 6 8 a2 2 + chr1 3 7 b1 1 - 1
chr1 14 17 a3 3 + chr1 12 16 b3 3 + 2
a::tiny_c.bed
chr1 1 4 a1 1 + chr1 2 5 c1 1 + 2
chr1 14 17 a3 3 + chr1 15 18 c3 3 + 2
a::tiny_d.bed
chr1 6 8 a2 2 + chr1 5 8 d1 1 + 2
chr1 14 17 a3 3 + chr1 15 18 d3 3 + 2
b::tiny_a.bed
chr1 3 7 b1 1 - chr1 1 4 a1 1 + 1
chr1 3 7 b1 1 - chr1 6 8 a2 2 + 1
chr1 12 16 b3 3 + chr1 14 17 a3 3 + 2
b::tiny_b.bed
chr1 3 7 b1 1 - chr1 3 7 b1 1 - 4
chr1 9 11 b2 2 + chr1 9 11 b2 2 + 2
chr1 12 16 b3 3 + chr1 12 16 b3 3 + 4
chr3 12 16 b3 3 + chr3 12 16 b3 3 + 4
b::tiny_c.bed
chr1 3 7 b1 1 - chr1 2 5 c1 1 + 2
chr1 9 11 b2 2 + chr1 10 13 c2 2 + 1
chr1 12 16 b3 3 + chr1 10 13 c2 2 + 1
chr1 12 16 b3 3 + chr1 15 18 c3 3 + 1
b::tiny_d.bed
chr1 3 7 b1 1 - chr1 5 8 d1 1 + 2
chr1 9 11 b2 2 + chr1 10 13 d2 2 + 1
chr1 12 16 b3 3 + chr1 10 13 d2 2 + 1
chr1 12 16 b3 3 + chr1 15 18 d3 3 + 1
tiny_a.bed tiny_b.bed tiny_c.bed tiny_d.bed
a 5 3 2 2
b 3 4 4 4
SUBTRACT
a = LOAD "tiny_a.bed";
b = LOAD "tiny_b.bed";
c = LOAD "tiny_c.bed";
e = a SUBTRACT b,c;
PRINT e;
f =COUNT e;
PRINT f;
Result
chr1 500 501 a4 4 +
chr2 500 501 a4 4 +
2
MERGEMAX
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
e = MERGEMAX a,b;
PRINT e;
f =COUNT e;
PRINT f;
Result
chr1 1 8
chr1 9 11
chr1 12 17
chr1 500 501
chr2 500 501
chr3 12 16
6
MERGEMAX, SCORE,SUM
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
e = MERGEMAX a,b WHERE SCORE(SUM);
PRINT e;
f = COUNT e;
PRINT f;
Result
chr1 1 8 . 4 .
chr1 9 11 . 2 .
chr1 12 17 . 6 .
chr1 500 501 . 4 .
chr2 500 501 . 4 .
chr3 12 16 . 3 .
6
MERGEMAX, SCORE, MEDIAN
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
e = MERGEMAX a,b WHERE SCORE(MEDIAN);
PRINT e;
f=COUNT e;
PRINT f;
Result
chr1 1 8 . 1 .
chr1 9 11 . 2 .
chr1 12 17 . 3 .
chr1 500 501 . 4 .
chr2 500 501 . 4 .
chr3 12 16 . 3 .
6
MERGEFLAT, NAME, SCORE, COUNT
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
c = LOAD "../data/tiny_c.bed";
e = MERGEFLAT a,b,c WHERE NAME(COLLAPSE),SCORE(COUNT);
PRINT e;
Result
chr1 1 2 a1 1 .
chr1 2 3 a1;c1 2 .
chr1 3 4 a1;b1;c1 3 .
chr1 4 5 b1;c1 2 .
chr1 5 6 b1 1 .
chr1 6 7 b1;a2 2 .
chr1 7 8 a2 1 .
chr1 9 10 b2 1 .
chr1 10 11 c2;b2 2 .
chr1 11 12 c2 1 .
chr1 12 13 c2;b3 2 .
chr1 13 14 b3 1 .
chr1 14 15 a3;b3 2 .
chr1 15 16 a3;b3;c3 3 .
chr1 16 17 a3;c3 2 .
chr1 17 18 c3 1 .
chr1 500 501 a4 1 .
chr2 500 501 a4 1 .
chr3 12 16 b3 1 .
chr4 15 18 c3 1 .
MERGEMIN, NAME, SCORE, COUNT
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
c = LOAD "../data/tiny_c.bed";
e = MERGEMIN a,b,c WHERE NAME(COLLAPSE),SCORE(COUNT);
PRINT e;
Result
chr1 3 4 a1;b1;c1 3 .
chr1 6 7 b1;a2 2 .
chr1 10 11 c2;b2 2 .
chr1 12 13 c2;b3 2 .
chr1 15 16 a3;b3;c3 3 .
chr1 500 501 a4 1 .
chr2 500 501 a4 1 .
chr3 12 16 b3 1 .
chr4 15 18 c3 1 .
MERGEMIN, NAME, SCORE, FILTER
a = LOAD "../data/tiny_a.bed";
b = LOAD "../data/tiny_b.bed";
c = LOAD "../data/tiny_c.bed";
e = MERGEMIN a,b,c WHERE NAME(COLLAPSE),SCORE(COUNT);
f = FILTER e WHERE SCORE(>1);
PRINT f;
Result
chr1 3 4 a1;b1;c1 3 .
chr1 6 7 b1;a2 2 .
chr1 10 11 c2;b2 2 .
chr1 12 13 c2;b3 2 .
chr1 15 16 a3;b3;c3 3 .
JACCARD
a = LOAD "data/tiny_a.bed";
b = LOAD "data/tiny_b.bed";
c = LOAD "data/tiny_c.bed";
d = LOAD "data/tiny_d.bed";
e = a JACCARD b,c,d;
PRINT e;
Result
b c d
a 0.2 0.222222 0.040404
tiny_a.bed
chr1 1 4 a1 1 +
chr1 6 8 a2 2 +
chr1 14 17 a3 3 +
chr1 500 501 a4 4 +
chr2 500 501 a4 4 +
tiny_b.bed
chr1 3 7 b1 1 -
chr1 9 11 b2 2 +
chr1 12 16 b3 3 +
chr3 12 16 b3 3 +
tiny_c.bed
chr1 2 5 c1 1 +
chr1 10 13 c2 2 +
chr1 15 18 c3 3 +
chr4 15 18 c3 3 +
tiny_d.bed
chr1 5 8 d1 1 +
chr1 10 13 d2 2 +
chr1 15 18 d3 3 +
chr1 20 23 d4 4 +
chr1 25 28 d5 5 +
chr1 30 33 d6 6 +
chr1 35 38 d7 7 +
chr1 40 43 d8 8 +
chr1 45 48 d9 9 +
chr1 50 53 d10 10 +
chr1 55 58 d11 11 +
chr1 60 63 d12 12 +
chr1 65 68 d13 13 +
chr1 70 73 d14 14 +
chr1 75 78 d15 15 +
chr1 80 83 d16 16 +
chr1 85 88 d17 17 +
chr1 90 93 d18 18 +
chr1 95 98 d19 19 +
chr1 100 103 d20 20 +
chr1 105 108 d21 21 +
chr1 110 113 d22 22 +
chr1 115 118 d23 23 +
chr1 120 123 d24 24 +
chr1 125 128 d25 25 +
chr1 130 133 d26 26 +
chr1 135 138 d27 27 +
chr1 140 143 d28 28 +
chr1 145 148 d29 29 +
chr1 150 153 d30 30 +
chrX 150 153 d30 30 +