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fix(sprinzl): number a 4-nt variable loop 44, 45, 46, 48 - #44
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assign_sprinzl() used a fixed map from covariance-model columns to labels, which numbers a four-nucleotide loop 44, 46, 47, 48 whenever the gap falls at the column labelled 45. It now numbers the loop by its length, as it already does for the variable-arm e-positions. The bundled E. coli K-12 and T4 tables are regenerated: 8 of 87 and 1 of 8 tRNAs change, in the 46 and 47 labels only. T5, yeast and tRNAs with a variable arm are left for #43 and #40. Part of #43. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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The clover tests pass with this change: |
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Part of #43.
assign_sprinzl()labels covariance-model columns through a fixed table, so a four-nucleotide variable loop whose gap falls at the column labelled 45 came out as 44, 46, 47, 48. The convention, and GtRNAdb 3, is 44, 45, 46, 48.The loop is now numbered by its length, the way the variable-arm
epositions already are: when a tRNA has exactly four bases in columns 44, 45, 64, the insert after 64 and 65, and no variable arm, they are labelled 44, 45, 46, 48.Bundled tables regenerated with
data-raw/sprinzl.R's own alignment and labelling code: E. coli K-12 (8 of 87 tRNAs change) and T4 (1 of 8). Only the 46 and 47 labels change (to 45 and 46); every other column is identical.A regression test reads the two tables and fails if a tRNA without a variable arm still has 44, 46, 47, 48 and no 45. It fails on the old tables (8 of 87) and passes on the new ones.
Not done here
e-label convention is part of Sprinzl position mapping: choose one method and validate on E. coli/T4, yeast and human #40.I could not run
devtools::test()here: the R dependencies would not build on the cluster node (compilingfsfailed). The regeneration used the script's functions in a base-R harness because Biostrings was not installed, and I checked the new test's condition against the old and new tables directly.