Net file format to Bed

Question

[int11ap1]

I would like to transform a net file format to a non-redundant bed file format. I know there exists the netToBed executable, but it only gives chromosome - start - end besides of including all parents and children thus being redundant (Since lines overlap).

I would like to have chromosome - start - end - target chromosome in the other species - strand. For that, I used

egrep "^ fill|^net" netfile | awk '{if ($0~/^net/) {chr=$2 ; next} ; print chr"\t"$2"\t"$2+$3"\t"$4"\t"$5}' | sed 's/+//g' > alignment.bed

but this is incorrect as I do not consider children. How would you do that?

Thank you.

Answer 1

[ivivek_ngs]

I do not think this should be able to do what you intend to, since the net file is not a properly tab delimited file. It is having indents describing the parent child relationships. So you can take a look at here or even here and try to perform the tasks.