parseGenBank {genbankr} | R Documentation

## 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"))

[Package genbankr version 1.16.0 Index]