gdb.export_fasta: Export a database genome as FASTA

In misha: Toolkit for Analysis of Genomic Data

Export a database genome as FASTA

Description

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

Usage

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.

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.

Value

Invisibly returns file.

See Also

gdb.init, gseq.extract

Examples

## Not run: 
gdb.init_examples()
out <- tempfile(fileext = ".fa")
gdb.export_fasta(out)
head(readLines(out))

## End(Not run)

misha documentation built on Feb. 20, 2026, 5:08 p.m.