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A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning

Source: R/asap_tbl.R
asap_tbl.Rd

asap_tbl() returns species partition hypothesis estimated by ASAP software (https://bioinfo.mnhn.fr/abi/public/asap/).

Usage

asap_tbl(
  infile,
  exe = NULL,
  haps = NULL,
  model = 3,
  outfolder = NULL,
  webserver = NULL,
  delimname = "asap",
  rank = NULL
)

Arguments

infile

Path to a FASTA file, or an object of class "asap" returned by asap(). When an "asap" object is supplied, the CLI path is skipped and best_partition() is called directly.

exe

Path to an ASAP executable. Ignored when infile is an "asap" object.

haps

Optional. A vector of haplotypes to keep into the tbl_df.

model

An integer specifying evolutionary model to be used. Available options are:

  • 0: Kimura-2P

  • 1: Jukes-Cantor (default)

  • 2: Tamura-Nei

  • 3: simple distance (p-distance)

outfolder

Path to output folder. Default to NULL. If not specified, a temporary location is used.

webserver

A .csv file containing ASAP results obtained from a webserver. Default to NULL.

delimname

Character. String to rename the delimitation method in the table. Default to 'asap'.

rank

Integer. Which ranked partition to return when infile is an "asap" object (default NULL selects rank 1 / best ASAP score). Ignored for CLI and webserver paths.

Value

an object of class tbl_df

Details

asap_tbl() relies on system to invoke ASAP software through a command-line interface. Hence, you must have the software available as an executable file on your system in order to use this function properly. asap_tbl() saves all output files in outfolder and imports the first partition file generated to Environment. Alternatively, asap_tbl() can parse a .csv file obtained from webserver such as (https://bioinfo.mnhn.fr/abi/public/asap/asapweb.html). The results file (webserver, or the file generated by the CLI run) is auto-detected: both ASAP's native format and the SPART matricial format (https://github.com/iTaxoTools/SpartParser) are accepted. A SPART file with more than one spartition yields one column per spartition, named {delimname}_1, {delimname}_2, etc.

References

Puillandre N., Brouillet S., Achaz G. 2021. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 21:609–620. doi:10.1111/1755-0998.13281

Author

Pedro S. Bittencourt, Tomas Hrbek

Examples


# \donttest{

#' # get path to fasta file
path_to_file <- system.file("extdata/geophagus.fasta", package = "delimtools")

# run ASAP
asap_df <- try(asap_tbl(infile = path_to_file, exe= "/usr/local/bin/asap", model= 3))
#> Error in asap_tbl(infile = path_to_file, exe = "/usr/local/bin/asap",  : 
#>   Please provide a valid path to the ASAP executable file.

# check
try(asap_df)
#> [1] "Error in asap_tbl(infile = path_to_file, exe = \"/usr/local/bin/asap\",  : \n  \033[1m\033[22mPlease provide a valid path to the ASAP executable file.\n"
#> attr(,"class")
#> [1] "try-error"
#> attr(,"condition")
#> <error/rlang_error>
#> Error in `asap_tbl()`:
#> ! Please provide a valid path to the ASAP executable file.
#> ---
#> Backtrace:
#>      ▆
#>   1. └─pkgdown::build_site_github_pages(...)
#>   2.   └─pkgdown::build_site(...)
#>   3.     └─pkgdown:::build_site_local(...)
#>   4.       └─pkgdown::build_reference(...)
#>   5.         ├─pkgdown:::unwrap_purrr_error(...)
#>   6.         │ └─base::withCallingHandlers(...)
#>   7.         └─purrr::map(...)
#>   8.           └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#>   9.             ├─purrr:::with_indexed_errors(...)
#>  10.             │ └─base::withCallingHandlers(...)
#>  11.             ├─purrr:::call_with_cleanup(...)
#>  12.             └─pkgdown (local) .f(.x[[i]], ...)
#>  13.               ├─base::withCallingHandlers(...)
#>  14.               └─pkgdown:::data_reference_topic(...)
#>  15.                 └─pkgdown:::run_examples(...)
#>  16.                   └─pkgdown:::highlight_examples(code, topic, env = env)
#>  17.                     └─downlit::evaluate_and_highlight(...)
#>  18.                       └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#>  19.                         ├─base::withRestarts(...)
#>  20.                         │ └─base (local) withRestartList(expr, restarts)
#>  21.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#>  22.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
#>  23.                         │   └─base (local) withRestartList(expr, restarts[-nr])
#>  24.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
#>  25.                         │       └─base (local) doWithOneRestart(return(expr), restart)
#>  26.                         ├─evaluate:::with_handlers(...)
#>  27.                         │ ├─base::eval(call)
#>  28.                         │ │ └─base::eval(call)
#>  29.                         │ └─base::withCallingHandlers(...)
#>  30.                         ├─base::withVisible(eval(expr, envir))
#>  31.                         └─base::eval(expr, envir)
#>  32.                           └─base::eval(expr, envir)
#>  33.                             ├─base::try(...)
#>  34.                             │ └─base::tryCatch(...)
#>  35.                             │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#>  36.                             │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#>  37.                             │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#>  38.                             └─delimtools::asap_tbl(infile = path_to_file, exe = "/usr/local/bin/asap", model = 3)

# }