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Annotate a mitogenome assembly with MitoFinder (WF2, optional)

Source: R/annotate_mitofinder.R
annotate_mitofinder.Rd

Runs MitoFinder in annotation-only mode (`-a`) on an existing assembly, independent of which assembler produced the contigs. Parses MitoFinder's feature-level GFF output into the common MitoPilot annotation data frame so the calls can be deduplicated against the other annotation tools. MitoFinder is treated as the lowest-priority tool by `annotate()` (it only fills gaps the higher-priority tools left).

Usage

annotate_mitofinder(
  assembly = NULL,
  mitofinder_db = NULL,
  genetic_code = "2",
  new_genes = FALSE,
  allow_introns = FALSE,
  mitofinder_opts = "",
  cpus = 4,
  condaenv = NULL,
  workdir = NULL
)

Arguments

assembly

a DNAStringSet object

mitofinder_db

path to a MitoFinder reference database (GenBank `.gb`), e.g. built with `custom_assembly_db(db_type = "mitofinder")`.

genetic_code

NCBI genetic code number (default: 2)

new_genes

logical; pass `–new-genes` to annotate non-standard genes (default: FALSE)

allow_introns

logical; pass `–allow-intron` to search for genes with introns (default: FALSE). See note above re: ruleset `intron = TRUE`.

mitofinder_opts

additional free-form command line options for MitoFinder

cpus

number of processors for MitoFinder (`-p`)

condaenv

conda environment containing MitoFinder, or NULL to run on PATH (default: NULL, mirroring the WF1 assembler call).

workdir

working directory for the MitoFinder run (default: a tempdir).

Value

a data frame with the common annotation columns (`contig, type, gene, product, pos1, pos2, length, direction, tRNA_ID, anticodon, start_codon, stop_codon, translation`). The codon/translation fields are populated for PCGs (mirroring `annotate_mitos2()`). Empty (correctly typed) when MitoFinder is off or finds nothing.

Details

Intron-containing genes annotated with `–allow-intron` are returned as multiple rows sharing one gene name (one per exon), matching the model used by `export.R` / `validate`. Only merged correctly downstream when the gene's curate ruleset has `intron = TRUE`; otherwise the exon rows are not merged.