Export the contig consensus sequences in a Sequencher project as FASTA

Writes one FASTA record per contig, named after the contig, holding its saved consensus sequence without gaps.

Usage

spf_contigs_to_fasta(path, file)

Arguments

path

Path to a Sequencher project file.

file

Path of the FASTA file to write.

Value

file, invisibly.

Details

The consensus is the one stored when the project was last saved, so it includes edits made up to then and none made later. Ambiguity codes are written as stored. The gapped consensus is not written, because each contig is gapped against its own alignment columns and the sequences do not form a shared alignment.

See also

read_spf_contigs(), spf_to_abif()

Examples

spf <- "project.SPF"
if (file.exists(spf)) spf_contigs_to_fasta(spf, tempfile(fileext = ".fasta"))