Download AnnoTALE's catalogue of TALE classes

A TALE class groups the TALEs of different strains that are similar enough to be considered the same effector, and carries the systematic name the literature uses for it (TalAA, TalAB, ...). AnnoTALE curates that catalogue and publishes it; this is an R wrapper around its 'AnnoTALEcli.jar loadAndView' call, which downloads the current definition. run_annotale_assign consumes what it writes.

Usage

run_annotale_load_classes(
  output_dir = tempfile("annotale_classes_"),
  class_builder = NULL,
  opt_param = "",
  java_args = "-Xms512M -Xmx8G",
  annotale_jar = .tantale_tool("annotale")
)

Arguments

output_dir

Directory where the catalogue will be written, created if it does not exist. The default is a new directory under tempdir(), which R deletes when the session ends: given how long the download takes, give a path you keep.

class_builder

Path to a class builder XML to read instead of downloading, as written by an earlier call. NULL, the default, downloads the current definition.

opt_param

A single string of further options for the tool, as key=value pairs separated by spaces. The keys this function sets itself (c, cb, outdir) are refused: use class_builder and output_dir.

java_args

A single string of options for the Java virtual machine, placed before -jar. The default raises the heap to 8 GB, which the catalogue needs (rebuilding it was seen to hold 1.8 GB resident); raise -Xmx if it runs out of memory.

annotale_jar

Path to the AnnoTALE jar file. The default is the copy tantale_setup() downloads; give a path to use another version.

Value

The path of the class builder XML, invisibly, so the call can be passed straight to run_annotale_assign. Beside it, output_dir also holds Lists_of_classes,_strains_and_TALEs/, whose List_of_classes.txt gives every class as plain text, one line per member with its aligned repeat-variable diresidues, strain and systematic name. That file answers "which class is this TALE in" without going through run_annotale_assign at all, when the TALE is already catalogued.

Details

The download is slow and bulky: about a quarter of an hour, and some 440 MB of output, most of it the class builder itself, which carries a cached alignment between every pair of catalogued TALEs. The file is therefore kept once and reused rather than fetched per call, which is what output_dir is for: point it at a directory you keep, and pass the returned path to run_annotale_assign as often as you like.

Record the date along with any class you take from it. A class name is stable, but the catalogue grows, and the index AnnoTALE appends to the class when it names a TALE (TalAH30, the thirtieth member of TalAH) is only true of the catalogue that produced it.

See also

run_annotale_assign, which places TALEs into these classes.

Other external TALE tools: run_annotale_assign(), run_annotale_build(), run_annotale_predict()

Examples

if (FALSE) { # interactive()
# Slow: downloads and rebuilds the catalogue, about 15 minutes.
classes <- run_annotale_load_classes(output_dir = tempfile("annotale_classes_"))
}