rduckhts_genbank_to_fasta: Write GenBank Sequence as FASTA

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Write GenBank Sequence as FASTA

Description

Writes the ORIGIN sequence of each record in a GenBank flat file to a FASTA file using the DuckHTS extension. Records are written under the same name rduckhts_genbank reports as seqname, so feature coordinates land on the contig of that name; the DEFINITION follows the name without its trailing period, as in NCBI's FASTA export. The FASTA is written to a temporary file beside output_path and renamed into place only after the input has been read to a clean end, so a failure never leaves a partial output and an existing file is never lost. Records without an ORIGIN block are skipped; zero written records is an error.

Usage

rduckhts_genbank_to_fasta(
  con,
  path,
  output_path = NULL,
  line_width = 70,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded
path	Path to the GenBank flat file, optionally bgzipped
output_path	Optional explicit output path for the FASTA file, one non-empty string; defaults to path with .fa appended
line_width	Sequence characters per output line, a whole number between 1 and .Machine$integer.max
overwrite	Logical. If TRUE, replace an existing output file; otherwise an existing output is an error

Value

A data frame with columns success, output_path and records_written

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.