helixforge stats

Inspect (read-only): before/after table of a Helixer vs HelixForge GFF3.

Works directly off two GFF3 paths (no rerun, no Mikado): it summarises the Helixer input and the reconciled output and tabulates the change. Pass --helixer-h5 to add the mean-Helixer-support row. Use this to show what reconciliation did; use benchmark for external accuracy metrics against a reference / BUSCO / OMArk.

Output (--out Markdown), one row per metric, columns: metric, helixer, helixforge, delta. Metric rows include gene and transcript counts, coding genes, isoforms/gene (mean/max), mono/multi-exon genes, CDS length (mean/median), % complete ORFs, mean AED, and mean Helixer support.

Options

Option	Description
--helixer	Helixer GFF3 (before). (required)
--reconciled	HelixForge GFF3 (after). (required)
--genome	Genome FASTA (optional).
--helixer-h5	Helixer HDF5 → populates the Helixer-support before/after column.
--out	Markdown summary output path. (default: before_after.md)

Examples

  # before/after on two GFF3s
  helixforge stats --helixer helixer.gff3 --reconciled helixforge.gff3 \
      --out before_after.md

  # add the Helixer-support column (needs the HDF5)
  helixforge stats --helixer helixer.gff3 --reconciled helixforge.gff3 \
      --helixer-h5 helixer.h5 --out before_after.md