Export a database genome as FASTA

Source: R/compute-sequence.R

Writes all contigs from a misha database to a multi-FASTA file.

gdb.export_fasta(
  file = NULL,
  groot = NULL,
  line_width = 80L,
  chunk_size = 1000000L,
  overwrite = FALSE,
  verbose = FALSE
)

Arguments

file

Output FASTA file path

groot

Optional database root path. If NULL, uses current database.

line_width

Number of bases per FASTA line. Default: 80.

chunk_size

Number of bases to extract per chunk while writing. Default: 1000000.

overwrite

Logical. If TRUE, overwrite existing output file. Default: FALSE.

verbose

Logical. If TRUE, prints progress messages. Default: FALSE.

Value

Invisibly returns file.

Details

By default, the currently active database is used. You can also provide groot to export another database without changing the caller's active database.

Examples

if (FALSE) { # \dontrun{
gdb.init_examples()
out <- tempfile(fileext = ".fa")
gdb.export_fasta(out)
head(readLines(out))
} # }