Create GenBank Feature Table — rduckhts

Creates a DuckDB table from a GenBank flat file using the DuckHTS extension. Features are emitted in read_gff's column shape, so a GenBank record substitutes for a GFF without a schema change. Locations built with join() or order() give one row per segment in biological order, complement(...) sets strand "-", and the GFF3 phase of each CDS segment is carried from /codon_start across segments. Parent links a feature to the gene sharing its /locus_tag wherever that gene appears in the record, repeated qualifiers become one key with comma-joined values, and valueless qualifiers read true. Records stream one at a time, and a record without a terminating // or with a malformed location is an error naming the feature and line.

Usage

rduckhts_genbank(
  con,
  table_name = NULL,
  path,
  attributes_map = FALSE,
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded
table_name: Name for the created table, or NULL to create the genbank_data view
path: Path to the GenBank flat file, optionally bgzipped
attributes_map: Logical. If TRUE, add a parsed MAP(VARCHAR, VARCHAR) column alongside the raw attribute string
overwrite: Logical. If TRUE, overwrites an existing table

Value

Invisible TRUE on success