#!/bin/bash

code=${1:-""}

[ "$code" == "" ] && echo "enter PDB id" && exit

[ -f ${code}.json ] && echo ${code} already processed && exit

xmlfile="/PATH_TO/PDB/validation_reports/${code:1:2}/${code}/${code}_validation.xml.gz"

if [ -f "${xmlfile}" ]
then
  zcat ${xmlfile} |sed 's/\t/  /g' | /home/jirka/bin/xq . >${code}.json
else
  echo "File \"${xmlfile}\" not found"
fi
