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jeromekelleher / sc2ts-paper

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Add Makefile commands to generate csv datafiles such as `data/long_arg_recombinants.csv` #208

Open hyanwong opened 1 week ago

hyanwong commented 1 week ago

We seem to have lost any code that creates this file, and we can't use the existing one for the new Viridian data. It is required for plotting. I think its just the output of the TreeInfo command.

It looks like the change that started referring to this now-missing file was here: https://github.com/jeromekelleher/sc2ts-paper/commit/7b2285d448bf4a2e563035820248439ef698cf9f#diff-04a5013aee36a31513cee04eb4b37ab3488e98d1f8cf40203b78b2cdbb797bdf

jeromekelleher commented 1 week ago

It's the output of the TreeInfo.recombinant_summary() function

hyanwong commented 1 week ago

Yep. I guess we should add something that generates that to the Makefile? Rather than doing it in plot.py?

jeromekelleher commented 1 week ago

Yeah. Let's hold off on that level of automation until the sc2ts APIs have finalised.

jeromekelleher commented 1 week ago

So, the idea is that the sc2ts repo has the inference and basic stats generation code, which we release on pypi. This repo has the code for running it on the viridian dataset, and the code for all the fancy stuff (which would be hard to maintain, keep working properly etc)