Bundle human Sprinzl coordinates from tRNAs-in-space #23
Description
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