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Rename the filenames in the BEAST2 options

Source: R/rename_beast2_options_filenames.R
rename_beast2_options_filenames.Rd

Rename the filenames in the BEAST2 options

Usage

rename_beast2_options_filenames(beast2_options, rename_fun)

Arguments

beast2_options

a set of BEAST2 options, that are the R equivalent of the BEAST2 command-line options, as can be created by create_beast2_options

rename_fun

a function to rename a filename, as can be checked by check_rename_fun. This function should have one argument, which will be a filename or NA. The function should return one filename (when passed one filename) or one NA (when passed one NA). Example rename functions are:

  • get_remove_dir_fun get a function that removes the directory paths from the filenames, in effect turning these into local files

  • get_replace_dir_fun get a function that replaces the directory paths from the filenames

  • get_remove_hex_fun get a function that removes the hex string from filenames. For example, tracelog_82c1a522040.log becomes tracelog.log

Value

a `beast2_options` with the filenames it contains renamed

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# beast2_options with local filenames
beast2_options <- create_beast2_options(
  input_filename = "my.fas",
  output_state_filename = "my_state.xml.state"
)
# Rename filenames to be in /my/new/folder
rename_beast2_options_filenames(
  beast2_options = beast2_options,
  rename_fun = beautier::get_replace_dir_fun("/my/new/folder")
)
#> $input_filename
#> [1] "/my/new/folder/my.fas"
#> 
#> $output_state_filename
#> [1] "/my/new/folder/my_state.xml.state"
#> 
#> $rng_seed
#> [1] NA
#> 
#> $n_threads
#> [1] NA
#> 
#> $use_beagle
#> [1] FALSE
#> 
#> $overwrite
#> [1] TRUE
#> 
#> $beast2_path
#> [1] "/github/home/.local/share/beast/lib/launcher.jar"
#> 
#> $verbose
#> [1] FALSE
#> 

check_empty_beaustier_folders()