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Fetch and parse NCBI GFF3 annotations and FASTA sequence for a BLAST top hit

Source: R/blast_ref_utils.R
fetch_blast_ref.Rd

Downloads the GFF3 record and, optionally, the FASTA sequence for the given accession from NCBI EFetch. The GFF3-derived annotations are written to output_file as a CSV suitable for ingestion into the blast_ref_annotations SQLite table. When sequence_file is supplied the raw nucleotide sequence (no FASTA header, no line-breaks) is written there for ingestion into the blast_ref_sequences table.

Usage

fetch_blast_ref(
  accession,
  output_file,
  sequence_file = NULL,
  genetic_code_file = NULL,
  json_file = NULL,
  blast_species = NULL,
  blast_evalue = NULL
)

Arguments

accession

NCBI accession number (e.g. "NC_012345.1")

output_file

path to write the annotations CSV

sequence_file

optional path to write the plain nucleotide sequence

genetic_code_file

optional path to write the NCBI translation table number

json_file

optional path to write a JSON bundle used by curation

blast_species

optional BLAST hit species label to include in JSON

blast_evalue

optional BLAST hit e-value to include in JSON