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Build a tales object from AnnoTALE's own TALE predictions

Source: R/tales_ingest.R
tales_from_annotale.Rd

Reads the output of AnnoTALE's analyze stage, as written by run_annotale_predict, and returns a validated tales object with the same columns as tales_from_telltales.

Usage

tales_from_annotale(
  annotale_dir,
  terminus_max_evalue = 1e-05,
  terminus_min_cover = 0.9,
  sanitize = FALSE,
  hmm_dir = system.file("extdata", "hmmProfile", package = "tantale", mustWork = TRUE)
)

Arguments

annotale_dir

A directory holding AnnoTALE analyze's TALE_Protein_parts.fasta, TALE_DNA_parts.fasta and TALE_RVDs.fasta, in it or in a subdirectory: the output_dir of run_annotale_predict() will do.

terminus_max_evalue, terminus_min_cover

Maximum hmmsearch E-value, and minimum fraction of the profile covered, for a terminal segment to be coded NTERM/CTERM. As in tell_tales, the match must also reach the end of the profile that adjoins the repeats.

sanitize

FALSE (default) keeps every array and warns about the anomalies; TRUE removes the arrays whose data are inconsistent or incomplete and keeps non-canonical TALEs (truncTALEs, for instance); "canonical" keeps canonical TALEs only. See tales and tales_anomalies.

hmm_dir

Directory holding the TALE terminus protein profiles.

Value

A validated tales object.

Details

AnnoTALE predict finds TALE genes in a genome; analyze splits each one into its N-terminal region, repeats and C-terminal region, and reads the RVD of every repeat. tell_tales runs analyze too, on ORFs it delimits itself from nhmmer hits of the TALE DNA profiles, so the two need not report the same set of TALEs.

As in tell_tales(), each terminal segment is searched with the TALE N- or C-terminal protein profile (hmmsearch, from the tantale environment; see tantale_setup). The rvd column holds NTERM/CTERM for a segment that is a canonical terminus by that search and XXXXX for any other (see tales_anchor_codes).

array_id is AnnoTALE's name for the TALE (MAI1-tempTALE1), without the location AnnoTALE appends to it. seqnames is filled when predict's GFF3 file is found under annotale_dir.

See also

Other TALE discovery: correct_tales(), tale_annotations, tales_from_telltales(), tell_tales()

Examples

# \donttest{
# Needs the tantale environment for hmmsearch (see tantale_setup()).
tales_from_annotale(system.file("extdata", "annotaleExampleOutput",
                                package = "tantale"))
#> <tales> 4 arrays, 96 parts
#>   layers: rvd   |   6 other columns
#>                                 rvd
#>   bai3_sample_tal_genomic_regions-tempTALE1  NTERM NN NG NN HD HD NI N* NG HD NI NG NN  ...
#>   bai3_sample_tal_genomic_regions-tempTALE2  NTERM NN HD NI NN HD NG HD HD NG NG NI NG  ...
#>   bai3_sample_tal_genomic_regions-tempTALE3  NTERM NN ND NN NI NK NN HD NN NG NG N* HD  ...
#>   bai3_sample_tal_genomic_regions-tempTALE4  NTERM NI HD NN NS NN NG HD NG HD NG NN NG  ...
# }