extract_seq.sh

#!/bin/bash
num=1
while read line; do
start=$(echo $line |cut -f 1 -d ",");
end=$(echo $line |cut -f 2 -d ",");
strand=$(echo $line |cut -f 3 -d ",");
  if [ "$strand" = "+" ]; then
     echo -e "253771435\t$((start - 3))\t${start}\t${num}\t0\t+";
  else
     echo -e "253771435\t$((${end} - 1))\t$((${end} + 2))\t${num}\t0\t-"
  fi
((num++))
done<$1