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G3viz / g3viz

Lollipop-diagram to interactively visualize genetic mutations
https://g3viz.github.io/g3viz/
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Pfam database is outdated #5

Open Jidgdoi opened 4 years ago

Jidgdoi commented 4 years ago

Hi,

Your "hgnc2pfam.rdb" is completely outdated, and so all lollipops mutations don't match correctly. It would be nice to update it, or in a more reliable and sustainable way, permit the user to query his own database or directly the Pfam website.

Otherwise, you did a nice and beautiful job to build this library !

Hope this message will reach you.

A fellow researcher.

phoeguo commented 4 years ago

Thank you for the suggestions. We will work on it shortly.

Nitin123-4 commented 4 years ago

Any update on this?

phoeguo commented 4 years ago

I have updated Pfam (v33.1) and UniProt (date: 2020-08-24) to latest version. Please update the package through GitHub and check the domain mapping.

Also, could you please teach me which gene is different from this package and cbioportal?

I will add some examples about how to retrieve or create domain mappings soon.

Nitin123-4 commented 4 years ago

Thanks for the update.

Jidgdoi commented 4 years ago

Many thanks for the update. The gene PIM1 was different, but with your update you fixed it. I didn't check for further genes but if I find some, I'll let you know.

I will add some examples about how to retrieve or create domain mappings soon.

This is a good point, I saw your "prepare_data" folder.