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")