naming conventions are jidnacked

[jmbilodeaux]

tRNA ID format reference (package inconsistencies)

Each clover function uses a different tRNA ID convention. Summary:

Function	Notation	Copy suffix	Example
read_sprinzl_coords()	RNA (U)	yes (-1-1)	tRNA-Arg-UCU-1-1
modomics_mods() $ref col	DNA (T)	yes (-1-1)	host-tRNA-Arg-TCT-1-1
plot_tRNA_structure() arg	DNA (T)	no	tRNA-Arg-TCT
structure_trnas()	DNA (T)	no	tRNA-Arg-TCT

Additional quirks:

• modomics_mods() prepends an organism prefix ("host-tRNA-", "phage-tRNA-") that
  read_sprinzl_coords() does not. Strip with str_remove("^[^-]+-tRNA-", "tRNA-").
• modomics_mods() uses "Ile" while read_sprinzl_coords() uses "Ile2" for the
  isoleucine subtype. Requires special-casing (see aa_mods / aa_raw split below).
• modifications$ref passed to plot_tRNA_structure() must exactly match the trna_id
  argument (first arg) — i.e. DNA notation, no copy suffix.

Workaround used here:
svg_id <- str_replace_all(sprinzl_id, "U", "T") |> str_remove("-\d+-\d+$")