Whole-array protein sequence, one per TALE array

Reassembles each array's parts (N-terminus, repeats and C-terminus, in order) into one full-length amino acid sequence, by pasting aa_seq together with no separator: the result is a real protein sequence, where tales_rvd_strings() joins RVD tokens with hyphens.

Usage

tales_get_protein_seq(x)

Arguments

x

A tales object carrying an aa_seq column.

Value

An Biostrings::AAStringSet, named by array_id.

Details

Parts are ordered by position_in_array. An alignment never reorders an array's parts, only inserts gaps between them, and a tales_msa's gaps are never rows: a gap is a column with no row for that array. So position_in_array gives the same part order alignment_position would, without needing to skip anything, and works unchanged whether x is a bare tales or a tales_msa.

See also

tales_get_dna_seq() for the DNA sequence sibling.

Other tales projections: tales_coded_strings(), tales_domain_codes(), tales_get_dna_seq(), tales_rvd_strings(), tales_to_universalmotif()

Examples

x <- tales_from_telltales(system.file("extdata", "tellTaleExampleOutput",
                                      package = "tantale"))
tales_get_protein_seq(x)[1]
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]  1434 MDPIRPRRPSPAREILPGPQPDR...GAADDFPAFNEEELAWLRELLPQ ROI_00001