parse.sh

#!/bin/bash

IFS=$'\t'

awk -F '\t' '{print $1 "\t" $4}' | while read -r line; do
  set -- $line
  id=$1
  json=$2
  metanetx=$(echo $json | jq -rM --unbuffered 'try (."MetaNetX (MNX) Equation" | .[] | .id) catch ""')
  kegg=$(echo $json | jq -rM --unbuffered 'try (."KEGG Reaction" | .[] | .id) catch ""')
  ec=$(echo $json | jq -rM --unbuffered 'try (."EC Number" | .[] | .id) catch ""')
  echo "$id,$metanetx,$kegg,$ec"
done