gff2bed.sh

#!/bin/bash
#take gff, choose annotation type, output bed-like file
#only argument is annotation type as a string

gzcat $1 | sed -e 's/;/\t/g' -e 's/:/\t/g' | awk -v var=$2 'BEGIN {OFS="\t"}{if ($3==var) print $1,($4-1),$5,$7,$8,$10}' |\
sort -k1,1 -k2,2n