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Find open reading frames in unannotated regions

Source: R/orf_finder.R
orf_finder.Rd

Optional annotation step (WF2) that runs after curation/validation. Uses NCBI ORFfinder to locate open reading frames, retains only those falling in regions without an existing annotation (allowing a user-set degree of overlap), keeps the longest ORF when several overlap the same unannotated region, and BLASTs each surviving ORF against the combined curation protein database so the annotate-details modal can show candidate gene identities. ORFs are written as annotations named `ORF.1`, `ORF.2`, ... with `type = "ORF"`.

Usage

orf_finder(
  annotations_fn = NULL,
  assembly_fn = NULL,
  genetic_code = "2",
  orffinder_opts = "-s 1",
  orffinder_condaenv = "orffinder",
  orf_min_len = 300,
  orf_max_overlap = 0.1,
  orf_nested = FALSE,
  ref_dir = ".",
  max_blast_hits = 10,
  blast_condaenv = "base",
  blast_ref_file = NULL,
  out_dir = NULL
)

Arguments

annotations_fn

Path to the (final, validated) annotations TSV.

assembly_fn

Path to the curated assembly FASTA.

genetic_code

NCBI translation table number (default: "2").

orffinder_opts

Extra ORFfinder command-line options (default: "-s 1"). `-g`, `-ml`, and `-n` are set automatically; do not include them here.

orffinder_condaenv

Conda environment containing ORFfinder (default: "orffinder"). Set NULL to use ORFfinder on the PATH.

orf_min_len

Minimal ORF length in nucleotides (default: 300).

orf_max_overlap

Maximum overlap with existing annotations, as a fraction of the ORF length, before an ORF is discarded (default: 0.1).

orf_nested

Logical; if TRUE pass -n false to ORFfinder so nested/overlapping ORFs are reported (default: FALSE).

ref_dir

Path to the curation reference directory (must contain a `featureProt/` subdirectory of per-gene protein FASTAs).

max_blast_hits

Maximum number of BLAST hits to retain per ORF (default: 10).

blast_condaenv

Conda environment containing blastp/makeblastdb (default: "base"). Set NULL to use them on the PATH.

blast_ref_file

Optional path to the staged `remote_blast_ref.json` for this sample. When supplied, the closest-relative reference's translated genes are injected into the per-gene FASTAs before the combined ORF database is built, so ORFs can also match the remote reference.

out_dir

Output directory for the ORF annotations TSV.