read_gff3: 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
)

Value

tibble

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