Skip to contents

Assign TALEs to AnnoTALE's published classes

Source: R/annotale.R
run_annotale_assign.Rd

An R wrapper around the 'AnnoTALEcli.jar assign' call. AnnoTALE places each TALE in the class of the catalogue it belongs to, and opens a new class for any that fit none. Where run_annotale_build groups the TALEs you hand it among themselves, knowing nothing of what the rest of the world calls them, this one answers "which published class is this TALE in", so its names can be compared with the literature's.

Usage

run_annotale_assign(
  fasta_file,
  class_builder,
  output_dir = tempfile("annotale_assign_"),
  strain = NULL,
  accession = NULL,
  opt_param = "",
  java_args = "-Xms512M -Xmx8G",
  annotale_jar = .tantale_tool("annotale")
)

Arguments

fasta_file

Path to a FASTA file of the TALEs to assign, one record per TALE (or per TALE part), in one of these forms:

  • full-length TALE coding sequences, such as the Predict/TALE_DNA_sequences_*.fasta file run_annotale_predict writes;

  • the corresponding protein sequences, such as its Predict/TALE_protein_sequences_*.fasta;

  • the parts of each TALE, one record per N-terminus, repeat and C-terminus, as in its Analyze/TALE_DNA_parts.fasta or Analyze/TALE_Protein_parts.fasta;

  • RVD sequences, the RVDs separated by hyphens (NI-HD-NG-NN-...), as in its Analyze/TALE_RVDs.fasta or the shipped Sample_TALEs_RVDSeqs_AnnoTALE.fasta (system.file("extdata", package = "tantale")).

class_builder

Path to the class builder XML holding the classes to assign against, as run_annotale_load_classes returns.

output_dir

Directory where output will be written, created if it does not exist. The default is a new directory under tempdir(), which R deletes when the session ends: give a path to keep the results.

strain

The strain the TALEs come from. AnnoTALE uses it to build the systematic names it proposes, so without it they are unnamed.

accession

The genome's accession number, recorded in the report.

opt_param

A single string of further options, as key=value pairs separated by spaces. The keys this function sets itself (t, c, s, a, outdir) are refused: use fasta_file, class_builder, strain, accession 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 reading the catalogue needs; 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

output_dir, invisibly. It holds the per-TALE assignment report, a table of original against proposed systematic names, a report and figure for each class that changed or was created, and a class builder extended with the TALEs given.

See also

run_annotale_load_classes, which fetches the classes; run_annotale_build, which builds classes from scratch instead.

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

Examples

if (FALSE) { # interactive()
# Needs a Java runtime and the catalogue, which takes a while to fetch.
classes <- run_annotale_load_classes(output_dir = tempfile("annotale_classes_"))
predicted <- run_annotale_predict(tantale_genome("MAI1"))
tales <- list.files(file.path(predicted, "Predict"),
                    pattern = "^TALE_DNA_sequences_", full.names = TRUE)
run_annotale_assign(tales, class_builder = classes, strain = "MAI1")
}