Write FASTA file of reference sequences.

Write FASTA file of reference sequences.

Usage

write_reference_fasta(regions_gr, output_path = NULL)

Arguments

regions_gr

A GRanges object including the sequences of the reference regions included for the data. This can be generated from the get_seq function.

output_path

The directory where the FASTA file should be written. Default is NULL, which will write the file to the current working directory.

Value

Writes a FASTA reference file "reference_output.fasta". If multiple ranges are included in the GRanges object, the sequences will be written to a single FASTA file. Sequences names will be the seqnames (contig) of the range.

Details

Generate an arbitrary multi-sequence FASTA file from GRanges including the reference sequences.

Examples

# Write FASTA files for the 20 genomic target sequences
# of TwinStrand's Mouse Mutagenesis Panel.
output_path <- tempdir()
rg <- get_seq("TSpanel_mouse")
#> Loading reference genome: BSgenome.Mmusculus.UCSC.mm10.
write_reference_fasta(rg, output_path = output_path)