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Runs the "predict" and "analyze" steps of AnnoTALE on a fasta file

Source: R/annotale.R
run_annotale_predict.Rd

An R wrapper around the AnnoTALE 'AnnoTALE.jar predict' and 'AnnoTALE.jar analyze' shell calls. run_annotale_build completes the AnnoTALE workflow.

Usage

run_annotale_predict(
  fasta_file,
  output_dir = tempfile("annotale_predict_"),
  prefix = NULL,
  opt_param = "Sensitive=false",
  java_args = "",
  annotale_jar = .tantale_tool("annotale")
)

Arguments

fasta_file

Path to a fasta file of the DNA sequences (e.g. a genome assembly) to search for TALEs.

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.

prefix

A scalar character vector containing a prefix that will be appended to TALE names by AnnoTALE. If not supplied, the function will try to guess the prefix from the input file name.

opt_param

A single string of options for the predict stage, as key=value pairs separated by spaces. AnnoTALE predict has one: Sensitive, false by default; "Sensitive=true" runs its sensitive scan. The keys this function sets itself (g, s, outdir) are refused: use fasta_file, prefix and output_dir. The analyze stage has no option of its own beyond a run name.

java_args

A single string of options for the Java virtual machine, placed before -jar in both stages. The default, "", leaves Java's own defaults (a heap of up to a quarter of the physical memory); give a -Xmx value, such as "-Xmx8G", if AnnoTALE 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, so that the call can be passed straight to tales_from_annotale(). If either stage exits with a non-zero status, the function stops with an error of class tantale_error_annotale_failed.

See also

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

Examples

# \donttest{
# Needs a Java runtime, and the tools and genomes tantale_setup() downloads.
fasta <- tantale_genome("MAI1")
out <- file.path(tempdir(), "annotale_predict_example")
run_annotale_predict(fasta, output_dir = out)
#> Running AnnoTALE predict for "MAI1"
#>   java -jar
#>   '/home/cunnac/snap/codium/495/.local/share/R/tantale/tools-1/AnnoTALEcli-1.5.jar'
#>   predict Sensitive=false
#>   g='/home/cunnac/snap/codium/495/.local/share/R/tantale/genomes-1/MAI1.fa'
#>   s='MAI1' outdir='/tmp/RtmpEQXqY1/annotale_predict_example/Predict'
#> Running AnnoTALE analyze for "MAI1"
#>   java -jar
#>   '/home/cunnac/snap/codium/495/.local/share/R/tantale/tools-1/AnnoTALEcli-1.5.jar'
#>   analyze
#>   t='/tmp/RtmpEQXqY1/annotale_predict_example/Predict/TALE_DNA_sequences_(MAI1).fasta'
#>   outdir='/tmp/RtmpEQXqY1/annotale_predict_example/Analyze'
list.files(file.path(out, "Predict"))
#> [1] "GFF__TALE_predictions_(MAI1).gff3"   "Genbank__TALE_predictions_(MAI1).gb"
#> [3] "TALE_DNA_sequences_(MAI1).fasta"     "TALE_protein_sequences_(MAI1).fasta"
#> [5] "protocol_predict.txt"               
# }