I want to count the base pairs of CNVs in bedfile B that overlap bedfile A preferably in bedtools in one line.
bedfile A:
chr1 100 500
bedfile B:
chr1 50 99
chr1 250 299
Result:
chr1 100 500 100
Thanks
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QVINTVS_FABIVS_MAXIMVS
Via BEDOPS bedmap --bases:
$ bedmap --echo --bases --delim '\t' A.bed B.bed > answer.bed
Make sure your inputs are sorted per BEDOPS sort-bed. Not sure what happens with other tools and sort-bed is the faster of the options, anyway.
Note that the base count is not unique, if elements in B overlap amongst themselves. You could pre-process the B set with bedops --merge to get a unique base count. Here's a one-liner to demo that use case:
``` $ bedops --merge B.bed \ | bedmap --echo --bases --delim '\t' A.bed - \
> unique_answer.bed
Or you could do process substitution, if you use bash:
$ bedmap --echo --bases --delim '\t' A.bed <(bedops --merge B.bed) > unique_answer.bed
Cool this is exactly what I want. I do already sort and merged file B to make things easier.
Is there a BEDOPS python api?
You could use the subprocess module.
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Alex Reynolds
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