create_directories_and_file_paths: Create directories and file paths
In Moritz-Kohls/virDisco2: Virus Discovery

Description Usage Arguments Value Examples

To prepare the simulation, the user needs to specify the directory containing the sam-files and the directory containing the excel result files from the prior mapping results. The simulation result files will be stored in the metasimulations directory which the user must specify, too. The R-function create_directories_and_file_paths creates subdirectories in the metasimulations directory and stores the directories and file paths needed later as global variables.

create_directories_and_file_paths(
  sam.directory,
  excel.directory,
  metasimulations.directory
)

`sam.directory`	Directory of the sam-files with original mapping results
`excel.directory`	Directory of the excel-files with mapped viruses information
`metasimulations.directory`	Directory of the files produced by simulation procedure

None

# Create new folders "sam_directory", "excel_directory" and "metasimulations_directory" at the desktop,
# extract the sam-file to the sam-directory and copy the excel-file to the excel-directory.
{
if ( Sys.info()[1] == "Windows") {
desktop.directory = file.path(Sys.getenv("USERPROFILE"))
desktop.directory = gsub("\\\\","/",desktop.directory)
desktop.directory = paste0(desktop.directory,"/Desktop")
my.sam.directory = paste0(desktop.directory,"/sam_directory")
my.excel.directory = paste0(desktop.directory,"/excel_directory")
my.metasimulations.directory = paste0(desktop.directory,"/metasimulations_directory")
}
else if ( Sys.info()[1] == "Linux") {
desktop.directory=system("xdg-user-dir DESKTOP",intern = T)
my.sam.directory = paste0(desktop.directory,"/sam_directory")
my.excel.directory = paste0(desktop.directory,"/excel_directory")
my.metasimulations.directory = paste0(desktop.directory,"/metasimulations_directory")
}
else {
my.sam.directory = file.choose() # Choose sam directory
my.excel.directory = file.choose() # Choose excel directory
my.metasimulations.directory = file.choose() # Choose metasimulations directory
}
}
dir.create(my.sam.directory)
dir.create(my.excel.directory)
unzip(zipfile = "./inst/extdata/NGS-12345_mapq_filtered.zip",exdir = my.sam.directory)
file.copy(from = "./inst/extdata/NGS-12345.xlsx",to = my.excel.directory)
create_directories_and_file_paths ( sam.directory = my.sam.directory , excel.directory = my.excel.directory , metasimulations.directory = my.metasimulations.directory )