Reference data

Parsing needs no reference data. Normalization does — it must read the transcript and genome sequences a description refers to. ferro prepare downloads and assembles them into a reference directory.

Prepare a reference

ferro prepare --output-dir ferro-reference

This downloads RefSeq transcripts, genome FASTAs, and cdot metadata, and writes them under ferro-reference/. A bare prepare builds a RefSeq-only reference — accessions NM_ / NR_ / NP_ / NG_.

Verify it

ferro check --reference ferro-reference

Optionally pre-build the on-disk cdot cache as a setup step, so the one-time cache build does not slow the start of a real (or timed) run:

ferro check --reference ferro-reference --build-cache

Optional data

Two opt-in flags provision more than RefSeq. Pass them at prepare time; both are incremental, so re-running prepare over an existing reference adds the requested data and preserves what is already there.

Ensembl support (accessions ENST / ENSG / ENSP) — downloads Ensembl cdot metadata and cDNA FASTAs (~1 GB+); off by default. Without it, an Ensembl input reports “Reference not found”:

ferro prepare --output-dir ferro-reference --ensembl

RefSeqGene placements — derives version-independent NG_ placements and the NG_→transcript-version map, required to resolve legacy gene-symbol selectors (NG_(GENE):c.…) and bare-NG_ hosted lookups:

ferro prepare --output-dir ferro-reference \
  --derive-ng-placements path/to/ng_accessions.txt

A fully-provisioned reference combines both in one run:

ferro prepare --output-dir ferro-reference --ensembl \
  --derive-ng-placements path/to/ng_accessions.txt

Using it

Point any normalizing command at the directory:

ferro normalize -i variants.txt --reference ferro-reference/

To guard against a reference that has drifted on disk, add --strict-reference, which hard-fails if the reference’s content no longer matches its recorded identity (the default warns and proceeds).