add make bed to tools.py, correct error in calling panel

[Emma-MacK]

• The core tool now includes make bed
• a function has been created to get HGNC ids from the panel json
• fix error in panel retriever, panelapp looks for Rcode without "R" so strip from code

[Emma-MacK]

The arguments needed for "get bed" personalisation have been hardcoded, but can be turned to command line arguments later

[EKPayne]

Line 139 of functions.py for HGNC in HGNC_list: full_url = url_base + str(HGNC)+ transcript_filter

HGNC should be lower case. Added here as a separate comment as this was added in a previous commit and I am therefore unable to comment directly within the code.

[EKPayne]

Additional thought: recommend adding timeout arguments for any request.get statements

[Emma-MacK]

I have make the requested changes. Additionally I have added some error handling if the panelapp query returns an empty json meaning there are no HGNC IDs to extracts, and if the NGTD indicates genomewide testing, which leads to a syntax error while trying to extract HGNC IDs

[Emma-MacK]

Additional thought: recommend adding timeout arguments for any request.get statements

I have added timeout arguments to the get requests

[Emma-MacK]

I have resolved the merge conflicts

[EKPayne]

One additional note. It looks like json is imported twice in functions.py. Remove once.

[Emma-MacK]

requested changes have been made

[EKPayne]

Happy that all requested corrections have been addressed. Branch merged into developed. Pull request can be closed.