phylotools (version 0.2.2)

dat2fasta: Convert and Save sequence data frame to fasta file

Description

Convert and Save sequence data frame to fasta file.

Usage

dat2fasta(dat, outfile = "out.fasta")

Arguments

dat

data frame by read.phylip or read.fasta

outfile

a character string, representing the name of the fasta file to be generated

Value

This is a routine without return value.

Details

The column of the data frame must be: 1. seq.name, 2. seq.text, represent the name of the sequences, the content of the sequence, eg. ATCGGGAAC.

References

http://www.genomatix.de/online_help/help/sequence_formats.html

See Also

read.fasta,read.phylip

Examples

# NOT RUN {
cat(
">seq_2", "GTCTTATAAGAAAGAATAAGAAAG--AAATACAAA-------AAAAAAGA",
">seq_3", "GTCTTATAAGAAAGAAATAGAAAAGTAAAAAAAAA-------AAAAAAAG",
">seq_5", "GACATAAGACATAAAATAGAATACTCAATCAGAAACCAACCCATAAAAAC",
">seq_8", "ATTCCAAAATAAAATACAAAAAGAAAAAACTAGAAAGTTTTTTTTCTTTG",
">seq_9", "ATTCTTTGTTCTTTTTTTTCTTTAATCTTTAAATAAACCTTTTTTTTTTA",
file = "trn1.fasta", sep = "\n")

res <- read.fasta("trn1.fasta")
dat2fasta(res)
unlink("trn1.fasta")
unlink("out.fasta")
# }