Matching genomic intervals in two bed files

Question

[arsala521]

Hello everyone,

I am new to shell scripting and need to write a code for a task. I looked many relevant posts but couldn't figure out the solution.

I have 2 files with three columns. First column is chromosome number and 2nd and 3rd column give region on that chromosome for example Chr2 2 10 means 2 to 10 on Chr2. So file1 with three columns

Chr1    4    10
Chr1    3     8
Chr2    15   30
Chr5    1   20

and another file2 with three columns

Chr1    2    30
Chr2    5    40
Chr3    2    10

I want line in file2 to be printed the number of times file1 regions are within its region. In this case for example, line 1 of file2 will be printed twice as two of the regions of file 1 (1st 2 lines) are in this region; line 2 of file 2 will be printed once as only one region of file 1(line3) is within its region, and line 3 of file 2 will not be printed as no region of file 1 is within this region.

The output will be

Chr1    2    30
Chr1    2    30
Chr2    5    40

Please let me know if the question is unclear. Any help is highly appreciated.

Thank you

[GenoMax]

Take a look at bedtools (https://bedtools.readthedocs.io/en/latest/ ) and bedops (https://bedops.readthedocs.io/en/latest/ ) for these kind of operations. No additional code should be needed on your part other than using correct commands from these packages.