Package 'rgbio'

Title: High-Performance GenBank I/O using 'gb-io'
Description: Interfaces with the 'gb-io' Rust crate to provide fast reading and writing of GenBank files. Supports parsing of sequences, features, and metadata into R-friendly data structures.
Authors: Richard Stöckl [aut, cre] (ORCID: <https://orcid.org/0000-0002-0451-0652>)
Maintainer: Richard Stöckl <[email protected]>
License: MIT + file LICENSE
Version: 0.4.0
Built: 2026-05-27 15:13:23 UTC
Source: https://github.com/richardstoeckl/rgbio

Help Index

Read a GenBank file

Description

Reads one or more GenBank records and returns selected components in either Bioconductor, tidy, or base format.

Usage

read_gbk(
  file,
  format = "bioconductor",
  sequences = TRUE,
  features = TRUE,
  metadata = TRUE,
  records = NULL,
  validate = TRUE
)

Arguments

file

Character path to a GenBank file.
format

Output format. One of "bioconductor", "tidy", or "base".
sequences

Logical; include sequence data.
features

Logical; include feature annotations.
metadata

Logical; include record metadata.
records

Integer indices or character accession/name selectors.
validate

Logical; validate parsed records.

Value

A variable object based on selected components. Returns either a single object or a named list with sequences, features, and/or metadata.

Read a GenBank file

Description

Deprecated compatibility wrapper for read_gbk().

Usage

read_genbank(file)

Arguments

file

Path to a GenBank file.

Value

Parsed records in legacy list format.

Write GenBank records

Description

Writes GenBank records from sequence, feature, and metadata components.

Usage

write_gbk(
  file,
  sequences,
  features = NULL,
  metadata = NULL,
  append = FALSE,
  validate = TRUE,
  line_width = 80
)

Arguments

file

Character path to output file.
sequences

DNAStringSet or named character vector.
features

GRanges with type and qualifiers in mcols(), or tidy feature table with columns type, start, end, strand, qualifiers.
metadata

DataFrame, data.frame, or list with record metadata.
append

Logical; append to file.
validate

Logical; validate inputs.
line_width

Integer sequence line width.

Value

Logical TRUE on success.

Write a GenBank file

Description

Deprecated compatibility wrapper for write_gbk().

Usage

write_genbank(file, sequence, features, metadata = list())

Arguments

file

Path to output file.
sequence

Sequence string.
features

Feature table with columns key, location, qualifiers.
metadata

Metadata list.

Value

Logical TRUE on success.