write_fasta: Write a fasta file to directory to use for whatever, e.g.,...

In sckott/sacbox: sacbox

Description

Write a fasta file to directory to use for whatever, e.g., running Clustal for multiple sequences alignment.

Usage

write_fasta(sequences, fileout, format = "bayesian")

Arguments

sequences	A list of sequences.
fileout	A file to write to, e.g., mysequences.fas
format	one of Bayesian or maxlik (for maximum likelihood).

Examples

## Not run: 
# Note that they are all the same sequence
myseqs <- c("TCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATATCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATA",
	"TCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATATCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATA",
	"TCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATATCTTATTTACAATAGGAGGATTATCAGGAATTATATTATCAAATTCATCTATTGATATTATACTACACGATACTTATTACGTTATTGGACACTTTCATTATGTACTCTCAATA")
names(myseqs) <- c("Apis_mellifera","Homo sapiens","Helianthus annuus")
write_fasta(sequences=myseqs, fileout="myseqs.fas")

## End(Not run)

sckott/sacbox documentation built on Sept. 3, 2020, 7:22 p.m.