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vgteam / sequenceTubeMap

displays multiple genomic sequences in the form of a tube map
MIT License
180 stars 26 forks source link

Integrate with Jupyter Notebooks #116

Open adamnovak opened 3 years ago

adamnovak commented 3 years ago

There is a desire to use the tube map visualizations in Jupyter Notebooks. Apparently it is challenging to do because of the indices (maybe the need to index vg files before visualizing them?).

This issue is meant to track that integration work, and the necessary preliminary fixes in the tube map project.

One potential way to make integration easier would be to be able to run directly from any .vg file, since most of the formats now in them provide much more efficient loading than the old Protobuf format. There's no good reason I can see to force people with PackedGraph .vg files to make them into .xg files to query.

adamnovak commented 3 years ago

@mcolebrook What exactly do you need from the tube map side to support your Jupyter Notebook integration project?

dortaelliott commented 3 years ago

Hi @adamnovak , the idea is after sequencing a part of the covid-19 genome through vg, enter that output as a custom file in sequence tube map, all this automated by bash in the jupyter notebook.