Hi I have want to identify the extreme most positions in a bed file from a specific position in a window frame,
E.g. if base position is chrX 154029186 154029187, and if following are the overlapping positions from another bed file in a specified window frame , then the tool should spit out
chrX 154029165 154029172
and
chrX 154028990 154028999
since they are extreme most positions in the frame
chrX 154029186 154029187 chrX 154029165 154029172
chrX 154029186 154029187 chrX 154028981 154028992
chrX 154029186 154029187 chrX 154028991 154029002
chrX 154029186 154029187 chrX 154028981 154028990
chrX 154029186 154029187 chrX 154028991 154029000
chrX 154029186 154029187 chrX 154028982 154028991
chrX 154029186 154029187 chrX 154028990 154028999
•
written
by
Aishwarya Kulkarni
2 answers
I think for a simple min-max search (it seems you want the find the row with smallest start and the one with the largest end) a oneliner in awk would work well:
cat data.bed | awk ' BEGIN { min=1E10 } $2 < min { min=$2; min_row=$0 } max < $3 { max =$3; max_row=$0 } END { print min_row; print max_row;}'
but it could be that I misunderstood what you want.
Advice: when you create an example make sure to make it simple, for example use an example with short readable numbers 100, 200 etc rather than something large that is difficult to parse/compare.
•
written
by
Istvan Albert
I don't really understand the format of your dataset. However, an alternative is to calculate the distances between target and query elements with awk and write that value to an additional column. Use GNU sort to sort that column and then take the head or tail, depending on whether the minimum or maximum value is needed.
•
written
by
Alex Reynolds
Log in to answer this question.
If I understood clearly then you have two bed files (e.g. "A.bed" and "B.bed") and you want to print only those co-ordinates of A.bed which doesn't overlap with B.bed.
If it is so then just do (install bedtools)
Your best bet is to either script something with pybedtools or with R (in GenomicRanges). If the BED files are large, the former is probably more efficient.
Assuming your bedfiles are sorted correctly you can pipe your intersections into
but there should be better way solving this.