get GO slims from GSEAbase for Panopea-generosa-genes-annotations.tab

[shellywanamaker]

use this file https://github.com/hputnam/Geoduck_Meth/blob/master/RAnalysis/Data/Genome/Panopea-generosa-genes-annotations.tab to pull GO slims for all go terms while keeping gene associations

[shellywanamaker]

This code generates a file that contains GO slim terms for each gene:

https://github.com/hputnam/Geoduck_Meth/blob/master/RAnalysis/Scripts/GO2GOslim.Rmd

[shellywanamaker]

I currently am running this R script GO2GOslim.R on Mox because the Rmd linked above was slow running on my computer. I'm realizing it's also slow on Mox as the script output log (output.txt) shows it's got through 29K/35K genes in almost 3 days of run time.

I came across this article https://www.r-bloggers.com/strategies-to-speedup-r-code/ and realize I can make some serious improvements to this code to decrease the run time.

Will post optimized code and hopefully results after making improvements suggested by the article above.