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
pathwith.faappended- 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