palm integration (mirroring lik.py in palm)#9
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standard-aaron wants to merge 11 commits intomasterfrom
Open
palm integration (mirroring lik.py in palm)#9standard-aaron wants to merge 11 commits intomasterfrom
lik.py in palm)#9standard-aaron wants to merge 11 commits intomasterfrom
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I tested this out locally (with input examples available from the repo) and got expected results & successfully saved the output in the
.quad_fit.npyformat needed for PALM. The usage looks like:python inference.py --ancientSamps example/exampleAncientSamps3.txt --timeBins example/timeBins200.txt --lik --out testwhich saves a
test.quad_fit.npyfile that summarizes the likelihood surface for that particular SNP. (PALM will require you to generate.quad_fit.npyfor each locus you want to include in your likelihood*)You should be able to follow the instructions on the PALM wiki to format the GWAS summary statistics and (after having run
clues/inference.py --likas demoed above) you should be able to runpalm.py.*Yes, it's pretty dumb that I generate these separately & save these as separate files. I was younger and dumber when I wrote this code. Alas, I don't have time to go back and take on the refactoring to make this simpler.