marin-dna/zoonomia-v1-val_enhancer

bolinas-dna/zoonomia-v1-val_enhancer

Conservation pre-filtered, case-encoded human-genome validation set from the `snakemake/zoonomia_projection_dataset` pipeline (commit `main`).

This is one of seven per-recipe validation parquets (val_cds, val_utr5, val_utr3, val_ncrna, val_promoter, val_enhancer, val_tss_pc) built from the same human-anchored phyloP_447m scoring used to create the cross-mammal training sets `bolinas-dna/zoonomia-v1-v1` and `bolinas-dna/zoonomia-v1-v2`.

Recipe (val_enhancer)

Enhancer regions defined by ENCODE cCRE V4 Enhancer-Like Signature classes (proximal pELS + distal dELS). Each cCRE is centered and resized to exactly 255 bp, then every annotated exon is subtracted (get_exons from Ensembl r115, no biotype filter). Stricter than the corresponding training-set recipe (get_exons_for_masking), which keeps low-quality / retained-intron exons scannable for new enhancer prediction; for validation we want a clean enhancer probe, so any exonic annotation disqualifies a base.

Schema

Sequence case encoding

For each base in seq:

• —Uppercase (A / C / G / T / N): the phyloP447m score at this position is `>= 2.2162` (the calibrated conservation threshold for the 447-way Cactus alignment, set to match phyloP241m's passing-base proportion at 2.27).
• —Lowercase (a / c / g / t / n): either the phyloP score is below the threshold, or there is no alignment at this position (NaN in the bigWig — NaN >= t is False in NumPy, so unaligned bases are encoded as lowercase).

Uppercase positions are confidently conserved across mammals; lowercase positions are either non-conserved or unaligned, and the encoding does not distinguish those two cases.

Construction

1. 1.Build region BED from Ensembl release 115 (canonical transcripts, where applicable) or ENCODE cCRE V4 — see Recipe above.
2. 2.Intersect with defined regions (genome minus N).
3. 3.Tile into 255 bp non-overlapping windows (bedtools makewindows -w 255 -s 255).
4. 4.Score each window against phyloP_447m (UCSC 447-way Cactus, Zoonomia + primates).
5. 5.Conservation pre-filter: keep only windows with proportion_conserved >= 0.2 (i.e. at least 51 of the 255 bases pass the phyloP_447m threshold of 2.2162).
6. 6.Deterministic subsample to ≤ 16,384 rows (seed 42).
7. 7.Extract sequences from hg38 (Ensembl r115) via twoBitToFa -bedPos.
8. 8.Case-encode each base by its per-position phyloP_447m value.

No reverse-complement augmentation — each genomic region appears exactly once. (RC augmentation is a training concern; for evaluation we want deterministic per-locus rows.)

Caveats

• —Recipes are independent probes, not a partition. A small number of bases may appear in multiple recipes (e.g. a val_promoter PLS overlapping a val_utr5 5' UTR; an add_flank(20) on CDS extending into intronic splice signal that abuts a 3' UTR). Don't concatenate the seven parquets without dedup.
• —Lowercase is ambiguous. Lowercase letters could mean either "phyloP score is below threshold" or "no alignment at this position". The encoding does not distinguish.
• —Only autosomes + chrX + chrY are included; the mitochondrial contig is excluded.
• —The val_promoter and val_enhancer cCRE recipes are not restricted to canonical transcripts — those classes are transcript-independent and come directly from ENCODE SCREEN cCRE V4.

Source code

• —Pipeline: snakemake/zoonomia_projection_dataset (latest)
• —Pinned to this dataset's build: commit `main`
• —Library: bolinas.zoonomia_projection_dataset.validation
• —Conservation track: phyloP_447m (`hg38.phyloP447way.bw`)