read_gbk {gggenomes}

Read genbank files

Description

Genbank flat files (.gb/.gbk/.gbff) and their ENA and DDBJ equivalents have a particularly gruesome format. That's why read_gbk() is just a wrapper around a Perl-based gb2gff converter and read_gff3().

Usage

read_gbk(file, sources = NULL, types = NULL, infer_cds_parents = TRUE)

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.

Value

tibble