gggenomes: A Grammar of Graphics for Comparative Genomics

read_gff3

R Documentation

Read features from GFF3 (and with some limitations GFF2/GTF) files

Description

Files with ⁠##FASTA⁠ section work but result in parsing problems for all lines of the fasta section. Just ignore those warnings, or strip the fasta section ahead of time from the file.

Usage

read_gff3(
  file,
  sources = NULL,
  types = NULL,
  infer_cds_parents = is_gff2,
  sort_exons = TRUE,
  col_names = def_names("gff3"),
  col_types = def_types("gff3"),
  keep_attr = FALSE,
  fix_augustus_cds = TRUE,
  is_gff2 = NULL
)

Arguments

`file`	Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files ending in `.gz`, `.bz2`, `.xz`, or `.zip` will be automatically uncompressed. Files starting with `⁠http://⁠`, `⁠https://⁠`, `⁠ftp://⁠`, or `⁠ftps://⁠` will be automatically downloaded. Remote gz files can also be automatically downloaded and decompressed. Literal data is most useful for examples and tests. To be recognised as literal data, the input must be either wrapped with `I()`, be a string containing at least one new line, or be a vector containing at least one string with a new line. Using a value of `clipboard()` will read from the system clipboard.
`sources`	only return features from these sources
`types`	only return features of these types, e.g. gene, CDS, ...
`infer_cds_parents`	infer the mRNA parent for CDS features based on overlapping coordinates. Default TRUE for gff2/gtf, FALSE for gff3. In most GFFs this is properly set, but sometimes this information is missing. Generally, this is not a problem, however, geom_gene calls parse the parent information to determine which CDS and mRNAs are part of the same gene model. Without the parent info, mRNA and CDS are plotted as individual features.
`sort_exons`	make sure that exons/introns appear sorted. Default TRUE. Set to FALSE to read CDS/exon order exactly as present in the file, which is less robust, but faster and allows non-canonical splicing (exon1-exon3-exon2).
`col_names`	column names to use. Defaults to `def_names("gff3")` (see `def_names`).
`col_types`	column types to use. Defaults to `def_types("gff3")` (see `def_types`).
`keep_attr`	keep the original attributes column also after parsing tag=value pairs into tidy columns.
`fix_augustus_cds`	If true, assume Augustus gff with bad CDS IDs that need fixing
`is_gff2`	set if file is in gff2 format