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Generate export NCBI files

Source: R/export.R
export_files.Rd

Generate export NCBI files

Usage

export_files(
  group = NULL,
  IDs = NULL,
  fasta_header =
    paste("{ID} [organism={Taxon}] [topology={topology}] [mgcode={genetic_code}]",
    "[location=mitochondrion] {Taxon} mitochondrion, complete genome"),
  fasta_header_gene = paste("{ID} [organism={Taxon}] [mgcode={genetic_code}]",
    "[location=mitochondrion] {Taxon}"),
  out_dir = NULL,
  generateAAalignments = T,
  gene_export = F
)

Arguments

group

(optional) export group names

IDs

One or more sample IDs to export. If not provided all samples in the export group will be exported

fasta_header

Template for mitogenome fasta headers. Uses glue syntax (i.e. `...`) to insert values from the samples table

fasta_header_gene

Template for gene fasta headers. Uses glue syntax (i.e. `...`) to insert values from the samples table

out_dir

directory to save the exported files

generateAAalignments

Generate group-level amino acid alignments (default: TRUE)

gene_export

Export FASTAs and feature tables for individual genes? (default: FALSE)