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Run TALE target predictions on DNA sequence(s) using Talvez

Source: R/target_predictions.R
talvez.Rd

An R wrapper around the Talvez predictor Perl script. Takes a list of TALE RVD sequences and a fasta file of DNA sequences and runs Talvez.

Usage

talvez(
  rvd_seqs,
  subj_file,
  opt_param = "-t 0 -l 19",
  output_dir = NULL,
  talvez_dir = system.file("tools", "TALVEZ_3.2", package = "tantale", mustWork = T),
  conda_bin = "auto"
)

Arguments

rvd_seqs

Tale RVD sequences are supplied as either a fasta file (atomic character vector) with Tale info (name) in title and sequences of RVD as a space or '-' separated string or as a Biostrings XStringSet with sequences of RVD similarly formatted.

subj_file

Expects a character vector specifying the path to the fasta file holding subject DNA sequence(s). Talvez does not accept sequences wrapped at a fixed width. The function unwraps them with Biostrings, but this fails for subject sequences longer than 20 kb: unwrap such sequences beforehand.

opt_param

An atomic character vector specifying optional parameters for the Talvez script (eg "-t 0 -l 19"). These may not include the '-e' and '-z' options specifying the matrix files.

output_dir

Expects a character vector specifying the path to an output directory. If not supplied, output files will be temporary.

talvez_dir

If you want to use another version of Talvez than the one supplied with tantale, specify the path of the directory containing the necessary files here.

conda_bin

Path to your Conda binary file if you need to specify a path different from the one that is automatically searched by the reticulate package functions.

Value

A tibble with one row per predicted EBE (effector binding element), the columns renamed from the tool's own output so that talvez and preditale return the same ones in the same order: tale_id, rvds, subj_seq_id, start, end, strand, ebe_seq and score, followed by the tool's own column: rank, the site's rank among the TALE's predictions by score.

Details

This wrapper uses the RVD-nucleotide specificity matrices shipped with Talvez; custom matrices are not supported. The Talvez script runs in a conda environment providing its dependencies, created automatically on first use.

See also

Other target prediction: plot_target_preds(), preditale(), tales_predict_targets()

Examples

# \donttest{
# Needs the tantale conda environment, built on first use.
x <- tales_from_telltales(system.file("extdata", "tellTaleExampleOutput",
                                      package = "tantale"))
rvds <- tales_rvd_strings(x)
subj <- system.file("extdata", "cladeIII_sweet_promoters.fasta",
                    package = "tantale")
preds <- talvez(rvd_seqs = rvds, subj_file = subj)
#> Invoking Talvez using the following command:
#> '/home/cunnac/mamba/envs/tantale/bin/perl' TALVEZ_3.2.pl -t 0 -l 19 -e mat1 -z
#> mat2 'rvdSeqsTalvez_f737a158c31c4.tsv' 'cladeIII_sweet_promoters.fasta'
head(preds)
#> # A tibble: 6 × 9
#>   tale_id   rvds              subj_seq_id start   end strand ebe_seq score  rank
#>   <chr>     <chr>             <chr>       <dbl> <dbl> <chr>  <chr>   <dbl> <dbl>
#> 1 ROI_00001 NN-NG-NN-HD-HD-N… SWEET11p_9…   980  1006 -      TGTACC… 10.0      1
#> 2 ROI_00001 NN-NG-NN-HD-HD-N… SWEET14p_N…   160   186 -      TGTTTC…  6.35     2
#> 3 ROI_00002 NN-HD-NI-NN-HD-N… SWEET11p_9…  1395  1409 +      TGTACA…  6.96     1
#> 4 ROI_00002 NN-HD-NI-NN-HD-N… SWEET11p_9…  1489  1503 +      TCCAGC…  6.66     2
#> 5 ROI_00002 NN-HD-NI-NN-HD-N… SWEET11p_I…   135   149 +      TGCATC…  6.53     3
#> 6 ROI_00002 NN-HD-NI-NN-HD-N… SWEET11p_B…   130   144 +      TGCATC…  6.53     4
# }