This function reads data from a single GenBank file or directory with GenBank files. It allows selective extraction of information by specifying sections and features.
Arguments
- path
A string representing the file path to the target GenBank (.gbk) file or directory.
- sections
An optional vector of strings representing the names of specific sections within the GenBank file to extract (e.g., "LOCUS", "DEFINITION", "ACCESSION", "VERSION"). If `NULL` (the default), the function extracts all available sections.
- features
An optional vector of strings indicating specific feature types to extract from the FEATURES section of the GenBank file (e.g., "CDS", "gene", "mRNA"). If `NULL` (the default), the function extracts all feature types present in the FEATURES section.
- origin
A boolean flag; when set to `TRUE` (the default), the origin sequence data is included in the output.
Value
A list containing the contents of the specified sections and features of the GenBank file. Each section and feature is returned as a separate list element.
Examples
# \donttest{
# Path to example GenBank file in the package
genbank_file <- system.file(
"extdata",
"BGC0000001.gbk",
package = "geneviewer"
)
# Read all data from the example GenBank file
gbk_data <- read_gbk(genbank_file)
# Read only specific sections from the example GenBank file
gbk_data <- read_gbk(genbank_file, sections = c("LOCUS", "DEFINITION"))
# Read specific features from the FEATURES section of the example GenBank file
gbk_data <- read_gbk(genbank_file, features = c("gene", "CDS"))
# Read data without the origin sequence
gbk_data <- read_gbk(genbank_file, origin = FALSE)
# }