write_gff3 {gggenomes}

Write a gff3 file from a tidy table

Description

Write a gff3 file from a tidy table

Usage

write_gff3(
  feats,
  file,
  seqs = NULL,
  type = NULL,
  source = ".",
  score = ".",
  strand = ".",
  phase = ".",
  id_var = "feat_id",
  parent_var = "parent_ids",
  head = "##gff-version 3",
  ignore_attr = c("introns", "geom_id")
)

Arguments

feats

tidy feat table

file

name of output file

seqs

a tidy sequence table to generate optional ⁠##sequence-region⁠ directives in the header

type

if no type column exists, use this as the default type

source

if no source column exists, use this as the default source

score

if no score column exists, use this as the default score

strand

if no strand column exists, use this as the default strand

phase

if no phase column exists, use this as the default phase

id_var

the name of the column to use as the GFF3 ID tag

parent_var

the name of the column to use as GFF3 Parent tag

head

additional information to add to the header section

ignore_attr

attributes not to be included in GFF3 tag list. Defaults to internals: ⁠introns, geom_id⁠

Value

No return value, writes to file

Examples

filename <- tempfile(fileext = ".gff")
write_gff3(emale_genes, filename, emale_seqs, id_var = "feat_id")