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Resolve an NCBI accession to a MapToRef reference file

Source: R/map_to_ref_refs.R
maptoref_fetch_accession.Rd

Downloads the GenBank record for the accession from NCBI, so the reference carries its own topology.

Usage

maptoref_fetch_accession(accession, out_dir = ".", log_fn = NULL)

Arguments

accession

An NCBI nucleotide accession, with or without its version (for example NC_002333 or NC_002333.1). Case insensitive.

out_dir

Directory to write into; the file is placed in <out_dir>/maptoref/.

log_fn

Optional path to an assembler log file to append to.

Value

A list with file, source ("ncbi"), and the uppercased accession that was resolved. Stops when NCBI has no record.