write_fasta — write_fasta • strollur

Write a FASTA formatted sequence file

Usage

write_fasta(data, filename = NULL, degap = FALSE)

Arguments

data: A `strollur` object
filename: a string containing the name of the output file. Default = 'dataset_name'.fasta
degap: a logical. Default = FALSE. When degap = `TRUE`, all gap characters will be removed from the sequences.

Value

name of FASTA file

Examples


miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
write_fasta(miseq, tempfile())
#> [1] "/tmp/Rtmp1sax1K/file1bf938f64d2d"