get_sequences: Retrieves fasta sequences from NCBI nucleotide database.

In primerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs

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

primerTree documentation built on April 5, 2022, 5:07 p.m.