bedtools intersect for file with different number of columns

Question

[aishwaryamandava7]

I need to check for overlaps between two files. But one file has varying number of columns.
super 60 101781 103918
super 65 348854 349379
super 3 2544203 2545004
super 3 2543098 2543825
X 14165618 14166161
3R 24612608 24614026
3R 2469690 2470475
3L 9771023 9771316
3L 15124656 15125963
2R 19853744 19854184
3L 1420174 1420978
3L 1419671 1420267
3R 13192377 13193044
2L 19854873 19858561
2L 19851701 19852306
X 9708332 9708728
2R 9271660 9272005
3R 23869959 23870963
2R 18894367 18895781
X 405984 407575
3L 6400755 6401249
3R 7834329 7835065
3R 7833332 7833973
scaffold 4690 16095096 16095560
scaffold 4820 6183430 6184808
scaffold 4770 7757711 7758517
scaffold 4784 9786818 9787106
This is the error it threw: Error: line number 20 of file map_names.bed has 3 fields, but 4 were expected. What can be done?

Answer 1

[Alex Reynolds]

Use BEDOPS:

$ sort-bed A.unsorted.bed > A.bed
$ sort-bed B.unsorted.bed > B.bed
$ bedops --element-of 1 A.bed B.bed > answer.bed