### For reading.
read.seq <- function(file.name, forceDNAtolower = FALSE,
convertDNAtoupper = TRUE){
ret <- seqinr::read.fasta(file.name, forceDNAtolower = forceDNAtolower)
### Make sure everything is in upper case.
if(convertDNAtoupper){
ret <- lapply(ret, function(x){ dna.low2up(x) })
}
ret
} # End of read.seq().
read.phi.df <- function(file.name, header = TRUE, sep = "\t", quote = ""){
ret <- read.table(file.name, header = header, sep = sep, quote = quote,
stringsAsFactors = FALSE)
ret$phi <- as.double(ret$phi)
ret
} # End of read.phi.df().
write.seq <- function(seq.data, file.name){
seqinr::write.fasta(seq.data, names(seq.data), file.name)
invisible()
} # End of write.seq().
write.phi.df <- function(phi.df, file.name){
phi.df$phi <- as.double(phi.df$phi)
write.table(phi.df, file.name, quote = FALSE, sep = "\t", row.names = FALSE)
invisible()
} # End of write.phi.df().
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