hydra2bed.sh

#!/bin/bash

echo "track name=\"$(basename $1)\" description=\"hydra output\" useScore=0 colorByStrand=255,0,0 0,0,255 gffTags=on"
awk -F '\t' '{ \
        gsub("+", "forward", $9); \
        gsub("-", "reverse", $9); \
        print $1 FS $2 FS $3 FS "Name=" $7 ";Strand=" $9  ";numMapping=" $16 FS FS $9; }' $1
awk -F '\t' '{ 
        gsub("+", "forward", $10); \
        gsub("-", "reverse", $10); \
        print $4 FS $5 FS $6 FS "Name=" $7 ";Strand=" $10 ";numMapping=" $16 FS FS $10 }' $1