Motif frequency for each interval

Question

[jmckow1]

I would like to search Chip-seq intervals (BED, bigwig, ect) for the frequency of a preset motif. Ideally outputting new interval files, each containing intervals that posses the same number of motifs. Please reply with any recommendations as to the simplest way to accomplish this. Thank You.

[GouthamAtla]

Do you want to search a bed file with a known motifs and get the coordinates of matches ?

[jmckow1]

I want to "rank" each bed interval according to number of short motifs present in that interval. Then I would like to split the original BED file into subsets based on "rank" of interval. Right now to accomplish this I getFastaFromBed (Bedtools) and then I use a script I found searching BioStars (https://github.com/Farhat/patt_search). This approach seems a bit cumbersome, someone else may have a better way.