R Under development (unstable) (2023-08-15 r84956 ucrt) -- "Unsuffered Consequences"
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> #rm(list = c("get_available_annotation_files", "worm_cat_fun"))
> 
> # source("../R/worm_cat_controller.R")
> # source("../R/worm_cat_add_categories.R")
> # source("../R/worm_cat_fisher_test.R")
> # source("../R/worm_cat_acceptable_pvalues.R")
> # source("../R/worm_cat_bubble_plot.R")
> library(wormcat)
Loading required package: ggplot2
Loading required package: ggthemes
Loading required package: plyr
Loading required package: svglite
> 
> # Utility function to delete the directory if it exists
> delete_directory_if_exists <- function(directory_path) {
+   if (dir.exists(directory_path)) {
+     unlink(directory_path, recursive = TRUE)
+     message(paste("Directory", directory_path, "deleted."))
+   }
+ }
> 
> 
> file_to_process <- "/Users/dan/Downloads/sams-1_up.csv"
> title <- "sams-1 up"
> output_dir <- "~/wormcat_out"
> rm_dir <- FALSE
> #annotation_file <- "whole_genome_v2_nov-11-2021.csv"
> annotation_file <- "https://dphiggs01.github.io/Wormcat_data/data/whole_genome_v2_nov-11-2021.csv"
> input_type <- "Wormbase.ID"
> zip_files <- FALSE
> 
> 
> delete_directory_if_exists(output_dir)
Directory ~/wormcat_out deleted.
> 
> # Call the WormCat function
> cat("Calling wormcat\n")
Calling wormcat
> worm_cat_fun(file_to_process,
+              title,
+              output_dir,
+              rm_dir,
+              annotation_file,
+              input_type,
+              zip_files)
[1] "The file /Users/dan/Downloads/sams-1_up.csv cannot be found."
[1] "EXITING!"
NULL
> 
> 
> # Call the function to read and process CSV data
> result <- get_remote_annotation_files()
> 
> # Print the list of tuples
> for (tuple in result) {
+   cat(tuple[[1]], " : ", tuple[[2]], "\n")
+ }
Whole genome v2  :  https://dphiggs01.github.io/Wormcat_data/data/whole_genome_v2_nov-11-2021.csv 
ORF Only  :  https://dphiggs01.github.io/Wormcat_data/data/ORF_only_v2_nov-11-2021.csv 
Ahringer RNAi v2  :  https://dphiggs01.github.io/Wormcat_data/data/ahringer_v2_nov-11-2021.csv 
Orfeome RNAi v2  :  https://dphiggs01.github.io/Wormcat_data/data/orfeome_v2_nov-11-2021.csv 
Whole genome v1  :  https://dphiggs01.github.io/Wormcat_data/data/whole_genome_v1_jul-03-2019.csv 
Ahringer RNAi v1  :  https://dphiggs01.github.io/Wormcat_data/data/ahringer_v1_jan-02-2019.csv 
Orfeome RNAi v1  :  https://dphiggs01.github.io/Wormcat_data/data/orfeome_v1_jan-31-2019.csv 
> 
> proc.time()
   user  system elapsed 
   0.68    0.18    0.87