Read one or more GFF3 files into gene_data format

`file` reads a single GFF3 file; `files` reads multiple files at once and combines them. `files` accepts a character vector of literal paths and/or wildcard patterns (e.g. `"examples/gff3/*.gff3"`).

Usage

read_gff3(
  file = NULL,
  files = NULL,
  feature_types = "CDS",
  anno_from = c("product", "Name", "gene", "ID"),
  unstranded = c("plus", "drop")
)

Arguments

file: Optional path to a single GFF3 file.
files: Optional character vector of GFF3 files (literal paths and/or wildcard patterns). All matched files are read and combined.
feature_types: Character vector of feature types to keep, default `"CDS"`.
anno_from: Character vector of GFF3 attribute keys, tried in order to fill the `anno` column.
unstranded: Character, default `"plus"`.

Value

A data.frame with `seq_id`, `start`, `end`, `strand`, `anno` followed by `type`, `source`, `score`, `phase` and `attributes`.

Examples

library(ggchord)
gff <- tempfile(fileext = ".gff3")
writeLines(c(
  "##gff-version 3",
  "seqA  source  CDS  101  500  .  +  0  ID=cds1;product=hypothetical protein"
), gff)
read_gff3(gff)
#>   seq_id start end strand                 anno type source score phase
#> 1   seqA   101 500      + hypothetical protein  CDS source     .     0
#>                             attributes
#> 1 ID=cds1;product=hypothetical protein