get_sequences {primerTree}

Retrieves fasta sequences from NCBI nucleotide database.

Description

Retrieves fasta sequences from NCBI nucleotide database.

Usage

get_sequences(
  accession,
  start = NULL,
  stop = NULL,
  api_key = Sys.getenv("NCBI_API_KEY"),
  simplify = TRUE,
  .parallel = FALSE,
  .progress = "none"
)

Arguments

accession

the accession number of the sequence to retrieve

start

start bases to retrieve, numbered beginning at 1. If NULL the beginning of the sequence.

stop

stop bases to retrieve, numbered beginning at 1. if NULL the stop of the sequence.

api_key

NCBI api-key to allow faster sequence retrieval.

simplify

simplify the FASTA headers to include only the genbank accession.

.parallel

if 'TRUE', perform in parallel, using parallel backend provided by foreach

.progress

name of the progress bar to use, see 'create_progress_bar'

Value

an DNAbin object.

See Also

DNAbin