genbank_download_parse: Download and parse sequences from GenBank

In vaulot/dvutils: A set of utilities

Description

If the GenBank file does not exist it fetches and writes it. If the file exists it just reads it. It extracts the metadata and return into a a data frame.

Note: use only sequence_keep = TRUE for simple gene sequences, else it may crash

Usage

genbank_download_parse(
  accession,
  directory,
  sequence_keep = TRUE,
  store_file = FALSE
)

Arguments

accession	Character vector of accession numbers
directory	Character, directory name which must end by "/"
sequence_keep	Logical, if FALSE the sequence is not returned in the file data frame
store_file	Logical, if FALSE the file is not stored and the sequence is not returned in the file data frame

Value

Data frame with the metadata information.

Examples

gb_metadata <- genbank_download_parse(accession = c("JX015376", "JQ768406", "LT621940"), directory = "genbank/", sequence_keep=TRUE)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.