Bundle human Sprinzl coordinates from tRNAs-in-space

[jayhesselberth]

Summary

clover consumes tRNAs-in-space global coordinate files via read_sprinzl_coords(), but we're missing human Sprinzl coordinates despite already bundling human structure SVGs and human MODOMICS data.

Current state

Data type	E. coli	S. cerevisiae	H. sapiens	Others
Sprinzl coords	yes	yes (nuclear + mito)	no	no
Structure SVGs	yes (39)	yes	yes	no
MODOMICS	yes	yes	yes	+ mouse, fly, worm
Identity elements	yes	yes	partial	no

tRNAs-in-space now provides H. sapiens coordinates (416 nuclear + 22 mitochondrial tRNAs), which would complete organism support and unlock heatmap/landscape plots for human tRNAs.

Tasks

Near-term

• Bundle human Sprinzl coordinate files from tRNAs-in-space (inst/extdata/sprinzl/)
• Bundle human mitochondrial Sprinzl coordinates if available
• Track provenance of tRNAs-in-space coordinate files (version/commit used to generate them)
• Cross-validate clover's modomics_mods() pairwise alignment output against tRNAs-in-space pre-mapped MODOMICS annotations

Longer-term

• Verify Type II tRNA support (Leu, Ser, Tyr with extended variable arms, ~90 nt) — trna_regions() hardcodes region boundaries for standard Type I tRNAs; heatmaps and landscape plots may not handle the extended variable arm positions correctly
• Verify mitochondrial tRNA handling in plotting functions (some mt-tRNAs lack the D-arm or T-arm)
• Document or wrap the tRNAs-in-space workflow (R2DT + trnas_in_space.py) so users can generate coordinates for organisms beyond the bundled set
• Add citation/attribution for tRNAs-in-space in package documentation and DESCRIPTION