Finish up gene annotation rearrangement

[davmlaw]

I moved things into PyReference and PyHGVS, still need to:

• Update transcript versions wiki page
• Update annotation.html install instructions
• Make sure import_gene_annotation works on the new file produced from pyHGVS script
• Can then close issue Install from scratch and verify it all works #52

Imports are:

python3 manage.py import_gene_annotation --genome-build=GRCh37 --annotation-consortium=Ensembl --json-file pyhgvs_transcripts_ensembl_grch37.json.gz

Then finally:

PyReference:

• Move from bitbucket to Github?
• Update example page with wget example for latest Ensembl/RefSeq
• Make a new PyPi release - https://pypi.org/project/pyreference/

PyHGVS

• Dialog with people to try and take over the project?
• Fork and carry forward, calling it SeeDot?

[davmlaw]

Still need to writeup new steps for a gene annotation release

Though I think you could almost just include an URL and then use the existing data from that? Would simplify things a lot there

[davmlaw]

I emailed the owners of PyHGVS - jeffrey.tratner@gmail.com; chrisnbeaumont@gmail.com; matt_d.shirley@novartis.com;

Hi, thanks for your work on PyHGVS.

I've made a number of fixes, and new features, eg supporting alignment gaps, see counsyl/hgvs#60

It would be good if these could be shared with other PyHGVS users, however it looks like nobody is accepting pull requests. I assume this is because people have moved on since Counsyl was acquired.

All my changes (24 commits) are in pull request 54 but I am happy to break them up into individual bug fixes or features etc, and of course deal with any issues you raise during code reviews!

Some thoughts / options maybe?

• Can you get someone in Myriad genetics to take over the project and accept pull requests?
• If Counsyl is gone, and nobody inside Myriad genetics is maintaining it, perhaps move to a different owner and community maintenance model?
• You could give me commit access to the repo (after rename)?
• If none of these options work - perhaps my fork could become a successor project, and you give official blessing / link to me in the README? I've renamed my project to https://github.com/SACGF/seedot to distinguish it and can make new PyPi package releases etc.

My GitHub profile: https://github.com/davmlaw

One project is https://shariant.org.au - an Australian Genomics project to share classifications shared between Australian labs via API. - HGVS is a critical part of this, so will be active on the project / answering issues etc

[davmlaw]

PyReference - moved to GitHub, made new release

PyHGVS - emailed people about future of project, no answer as yet

VG Wiki - created pages:

https://github.com/SACGF/variantgrid/wiki/Gene-and-Transcript-Version-Data
https://github.com/SACGF/variantgrid/wiki/Generating-Transcript-Version-Data