write_gff3: Write a gff3 file from a tidy table

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

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

Examples

## Not run: 
write_gff3(emale_genes, "emales.gff", emale_seqs, id_var="feat_id")

## End(Not run)

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.