Skip to contents

Read Sprinzl coordinates from a global coordinates TSV file.

Source: R/sprinzl.R
read_sprinzl_coords.Rd

Read a tRNAs-in-space global coordinates file and return a tibble with standardized column names. These files map each position of each tRNA to its Sprinzl numbering, structural region, and global alignment index.

Usage

read_sprinzl_coords(path)

Arguments

path

Path to a global coordinates TSV file (may be gzipped).

Value

A tibble with columns:

  • trna_id: tRNA identifier (e.g., nuc-tRNA-Ala-AGC-1-1)

  • pos: 1-based position in tRNA body

  • sprinzl_label: Sprinzl position (character: "1", "20a", "47:e1", etc.)

  • global_index: cross-tRNA universal alignment position

  • region: structural region (acceptor-stem, D-stem, D-loop, etc.)

  • residue: reference nucleotide

Examples

path <- clover_example("sprinzl/sacCer_global_coords.tsv.gz")
coords <- read_sprinzl_coords(path)
coords
#> # A tibble: 19,967 × 6
#>    trna_id                pos sprinzl_label global_index region        residue
#>    <chr>                <dbl> <chr>                <dbl> <chr>         <chr>  
#>  1 nuc-tRNA-Ala-AGC-1-1     1 1                        1 acceptor-stem G      
#>  2 nuc-tRNA-Ala-AGC-1-1     2 2                        2 acceptor-stem G      
#>  3 nuc-tRNA-Ala-AGC-1-1     3 3                        3 acceptor-stem G      
#>  4 nuc-tRNA-Ala-AGC-1-1     4 4                        4 acceptor-stem C      
#>  5 nuc-tRNA-Ala-AGC-1-1     5 5                        5 acceptor-stem G      
#>  6 nuc-tRNA-Ala-AGC-1-1     6 6                        6 acceptor-stem T      
#>  7 nuc-tRNA-Ala-AGC-1-1     7 7                        8 acceptor-stem G      
#>  8 nuc-tRNA-Ala-AGC-1-1     8 8                        9 unknown       T      
#>  9 nuc-tRNA-Ala-AGC-1-1     9 9                       10 unknown       G      
#> 10 nuc-tRNA-Ala-AGC-1-1    10 10                      11 D-stem        G      
#> # ℹ 19,957 more rows