Create a lazy table reference from a FASTA file

Streams a FASTA file of biological sequences as rows: one row per record with columns id, desc, and seq. id is the first whitespace-delimited token of the header line, desc is the remainder (an empty string when the header carries no description), and seq is the sequence with line breaks removed. Records stream one batch at a time, so a read set larger than RAM never fully materializes. Gzip-compressed files (.fasta.gz, .fa.gz) are read transparently. No data is read until collect() is called.

Usage

tbl_fasta(path, batch_size = .DEFAULT_BATCH_SIZE, quiet = FALSE)

Arguments

path: Path to a .fasta/.fa file, optionally gzip-compressed.
batch_size: Number of records per batch (default 65536).
quiet: If FALSE (default), report the record count when the scan completes.

Value

A vectra_node object representing a lazy scan of the FASTA file.

Details

The seq_* expression family (seq_revcomp(), seq_gc(), seq_translate(), seq_dist(), ...) operates on the seq column directly inside mutate()/filter(). See seq_expressions.

A record cut short is a loud error, not a silent drop: a header that is not the first non-blank token, or a byte where a > is expected, stops the scan. When the scan reaches the end of the file it reports the number of records read (suppress with quiet = TRUE).

Examples

f <- tempfile(fileext = ".fasta")
writeLines(c(">seq1 first", "ACGTACGT", ">seq2 second", "GGGGCCCC"), f)
node <- tbl_fasta(f, quiet = TRUE)
node |> mutate(gc = seq_gc(seq)) |> collect()
unlink(f)