Build a tales object from a tell_tales run directory

Reads the AnnoTALE/telltale part files of a single tell_tales output directory and returns a validated tales object.

Usage

tales_from_telltales(telltale_dir, sanitize = FALSE)

Arguments

telltale_dir

Path to a single tell_tales output directory.

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.

Value

A validated tales object.

Details

One row per part: the N-terminus, each repeat and the C-terminus, as AnnoTALE split the array's longest ORF. The rvd column holds the RVD of a repeat, or a terminus code (see tales_anchor_codes): NTERM/CTERM when the terminus is a canonical TALE terminal domain by the protein profile search of tell_tales, XXXXX when it is not. When AnnoTALE reported no terminus on one side, the array has no part there, with a warning. An array whose protein and DNA parts disagree is left out, with a warning.

A candidate array with a TALE terminus DNA hit that AnnoTALE could not split into parts is absent from the result, with a warning naming it. tales_anomalies cannot report such an array, since it is not in the object. After frameshift correction this usually means the array was corrected against a distant reference; see max_comparisons in tell_tales.

The directory must have been written by the current version of tell_tales(), whose array_report.tsv holds the terminus check; an older one is an error.

The result carries no dom_code: that surrogate key is minted later, by the relatedness computation, over the whole set of parts being analysed.

See also

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

Examples

tales_from_telltales(system.file("extdata", "tellTaleExampleOutput",
                                 package = "tantale"))
#> <tales> 4 arrays, 96 parts
#>   layers: rvd   |   6 other columns
#>              rvd
#>   ROI_00001  NTERM NN NG NN HD HD NI N* NG HD NI NG NN HD NI NG NI NG NN N ...
#>   ROI_00002  NTERM NN HD NI NN HD NG HD HD NG NG NI NG NI NG CTERM
#>   ROI_00003  NTERM NN ND NN NI NK NN HD NN NG NG N* HD N* HD NI NN HD NG H ...
#>   ROI_00004  NTERM NI HD NN NS NN NG HD NG HD NG NN NG HD NS HD NI NG HD H ...