parseGenBank: Parse raw genbank file content

In gmbecker/genbankr: Parsing GenBank files into semantically useful objects

Parse raw genbank file content

Description

Parse genbank content and return a low-level list object containing each component of the file.

Usage

parseGenBank(file, text = readLines(file), partial = NA, verbose = FALSE,
  ret.anno = TRUE, ret.seq = TRUE)

Arguments

file	character. The file to be parsed. Ignored if text is specified
text	character. The text to be parsed.
partial	logical. If TRUE, features with non-exact boundaries will be included. Otherwise, non-exact features are excluded, with a warning if partial is NA (the default).
verbose	logical. Should informative messages be printed to the console as the file is being processed.
ret.anno	logical. Should the annotations in the GenBank file be parsed and included in the returned object. (Defaults to TRUE)
ret.seq	logical. Should the origin sequence (if present) in the GenBank file be included in the returned object. (Defaults to TRUE)

Value

if ret.anno is TRUE, a list containing the parsed contents of the file, suitable for passing to make_gbrecord. If ret.anno is FALSE, a DNAStringSet object containing the origin sequence.

Note

This is a low level function not intended for common end-user use. In nearly all cases, end-users (and most developers) should call readGenBank or create a GenBankFile object and call import instead.

Examples

prsd = parseGenBank(system.file("sample.gbk", package="genbankr"))

gmbecker/genbankr documentation built on Oct. 30, 2023, 9:24 a.m.