Bash/Awk: Find common translocations in two files using overlapping coordinates

Question

I would like to compare two files to identified common translocations. However, these translocations don't have exactly the same coordinates between the files. So I want to see if the translocation occurs between the same pair of chromosomes (chr1, chr2) and if the coordinates overlap.

Here is an examples for two files:

file_1.txt:

chr1 min1 max1 chr2 min2 max2
1 111111 222222 2 333333 444444
2 777777 888888 3 555555 666666
15 10 100 15 2000 2100
17 500 530 18 700 750   
20 123456 234567 20 345678 456789

file_2.txt:

chr1 min1 max1 chr2 min2 max2
1 100000 200000 2 400000 500000
2 800000 900000 3 500000 600000
15 200 300 15 2000 3000
20 150000 200000 20 300000 500000

The objective is that the pair chr1 and chr2 is the same between file 1 and file 2. Then the coordinates min1 and max1 must overlap between the two files. Same thing for min2 and max2.

For the result, perhaps the best solution is to print the two lines as follows:

1   111111  222222  2   333333  444444
1   100000  200000  2   400000  500000

2   777777  888888  3   555555  666666
2   800000  900000  3   500000  600000

20  123456  234567  20  345678  456789
20  150000  200000  20  300000  500000

(For this simplified example, I tried to represent the different types of overlap I could encounter. I hope it is clear enough).

Thank you for your help.

I'd probably reach for Perl or Python to solve this problem. It's too hairy for bash or awk, and if you are able to find a bash solution, it will be very hard to maintain it. — choroba
do both the chr1 and chr2 data sets need to 'overlap` or just one of the two data sets? how big are these files (in terms of MBytes?) - wondering if one of the data sets can be stored in memory — markp-fuso
The files are not large. They are all about 10 MB in size, and each has about 100 lines. The coordinates of chr1 in file_1 must overlap those of chr1 in file_2. The same goes for the coordinates of chr2 in file_1, which must overlap those of chr2 in file_2. This is an approximation to make sure that it is the same translocation event between the two chromosomes. Don't hesitate to ask me if you need more details. — Leafou

karakfa karakfa · Accepted Answer · 2021-04-13T15:15:51

awk to the rescue!

$ awk 'function overlap(x1,y1,x2,y2) {return y1>x2 && y2>x1}
             {k=$1 FS $4}
     NR==FNR {r[k]=$0; c1min[k]=$2; c1max[k]=$3; c2min[k]=$5; c2max[k]=$6; next}
     overlap(c1min[k],c1max[k],$2,$3) &&
     overlap(c2min[k],c2max[k],$5,$6) {print r[k] ORS $0 ORS}' file1 file2

1 111111 222222 2 333333 444444
1 100000 200000 2 400000 500000

2 777777 888888 3 555555 666666
2 800000 900000 3 500000 600000

20 123456 234567 20 345678 456789
20 150000 200000 20 300000 500000

assumes the first file can be held in memory and prints an extra empty line at the end.

Bash/Awk: Find common translocations in two files using overlapping coordinates

1 Answers