I noticed that CUSIPs can be linked to CIK codes. See Ian Gow's repo https://github.com/iangow-public/edgar
I use a slightly different approach - I store the data on csv format.
Step 1: run this curl script to download the SEC form files.
curl -k -o "form#1.zip" "https://www.sec.gov/Archives/edgar/full-index/[2000-2017]/QTR4/form.zip"
Step 2: after unpacking the forms run, the linesform.py script to extract the urls for SC 13D and SC 13G forms.
Step 3: run the perl script to extract the CUSIPS that belwong to a CIK.