R/global.R

In iofeidis/tripr: T-cell Receptor/Immunoglobulin Profiler (TRIP)

## global.R

## New environment for maintenance of state across function calls
e <- new.env(parent = parent.env(environment()))
    
## Declare global variables
e$all_used_columns <- NULL
e$used_columns <- NULL
e$output_folder <- NULL
Functionality <- NULL
dataInputColumnsTemp <- NULL
seq1 <- NULL
seq2 <- NULL
e$msg <- NULL
SpecificConvergentEvolution <- NULL
Freq <- NULL
freqTables_datasets <- NULL
motif_datasets <- NULL
motif_all <- NULL
Summary.V.REGION.identity.. <- NULL
Summary.Sequence <- NULL
cluster_id <- NULL
germline <- NULL
productive <- NULL
clonotype <- NULL
N <- NULL
Num_of_patients <- NULL
start_char <- NULL
end_char <- NULL
SHM_high_similarity <- NULL
filteredData_id <- NULL
mutational_status_table_allData <- NULL
cl_ids_logos <- NULL
frequenciesTables_results_cl <- NULL
mutation_results_nt <- NULL
higly_sim_clonotypes_barchart_down_threshold <- NULL
cdr3_length_distribution <- NULL
e$pi_distribution <- NULL
logo_plot <- NULL
logo_per_region <- NULL
Dataset <- NULL
logo_result_cl <- NULL
logo_per_region_cl <- NULL
logFile <- NULL

tmp_path <- getwd() # change it to "/tmp" for server

num_of_cores <- parallel::detectCores(all.tests = FALSE, logical = TRUE) # change this to the custom number of threads

# logfile
# if (!file.exists(paste0(tmp_path, "/inst/extdata/log_files"))) {
#     fs::dir_create(paste0(tmp_path, "/inst/extdata/log_files"))
# }

# if (!file.exists(paste0(system.file("extdata", package="tripr"), "/log_files"))) {
#     fs::dir_create(system.file("extdata", package="tripr"), "log_files")
# }
# logFile <- paste0(system.file("extdata/log_files", package="tripr"), "/log_file_", trunc(as.numeric(Sys.time())), ".txt")
# logFile <- paste0(tmp_path, "/inst/extdata/log_files/log_file_", trunc(as.numeric(Sys.time())), ".txt")


# cat(paste0("Function", "\t", "Parameters", "\t", "Num of input rows", "\t", "Num of input columns", "\t", "Start time", "\t", "End time", "\t", "Memory used"), file = logFile, append = FALSE, sep = "\n")

use_only_useful_columns <- TRUE # libraries.R TRUE
save_lists_for_bookmark <- FALSE # libraries.R FALSE
save_tables_individually_filter_in <- FALSE # libraries.R TRUE
save_tables_individually <- TRUE # libraries.R TRUE

logfile <- function() {
    logFile <- paste0(system.file("extdata/log_files", package="tripr"), 
        "/log_file_", trunc(as.numeric(Sys.time())), ".txt")
    cat(paste0("Function", "\t", "Parameters", "\t", "Num of input rows", "\t", 
        "Num of input columns", "\t", "Start time", "\t", "End time", "\t", 
            "Memory used"), file = logFile, append = FALSE, sep = "\n")
    assign('logFile', logFile, envir = topenv())
}