Nothing
### Functions to read and write files.
read.fasta <- function(filename, byrow = TRUE, code.type = .code.type[1],
aligned = TRUE, sep = ""){
if(is.null(code.type)){
code.type <- "UNKNOWN"
}
if(code.type[1] == "CODON" && sep == ""){
sep <- ","
}
ret <- read.fasta.format(filename, byrow = byrow, aligned = aligned,
sep = sep)
### transfer data.
if(code.type[1] == "NUCLEOTIDE"){
ret$org <- code2nid(ret$org.code)
} else if(code.type[1] == "SNP"){
ret$org <- snp2sid(ret$org.code)
} else if(code.type[1] == "CODON"){
ret$org <- as.numeric(ret$org.code)
} else if(code.type[1] == "AMINO_ACID"){
ret$org <- acode2aid(ret$org.code)
}
if(any(code.type[1] %in% .code.type)){
ret$code.type <- code.type[1]
}
ret
} # End of read.fasta().
read.phylip <- function(filename, byrow = TRUE, code.type = .code.type[1],
sep = ""){
if(is.null(code.type)){
code.type <- "UNKNOWN"
}
if(code.type[1] == "CODON" && sep == ""){
sep <- ","
}
ret <- read.phylip.format(filename, byrow = byrow, sep = sep)
### transfer data.
if(code.type[1] == "NUCLEOTIDE"){
ret$org <- code2nid(ret$org.code)
} else if(code.type[1] == "SNP"){
ret$org <- snp2sid(ret$org.code)
} else if(code.type[1] == "CODON"){
ret$org <- as.numeric(ret$org.code)
} else if(code.type[1] == "AMINO_ACID"){
ret$org <- acode2aid(ret$org.code)
}
if(any(code.type[1] %in% .code.type)){
ret$code.type <- code.type[1]
}
ret
} # End of read.phylip().
write.fasta <- function(seqdata, filename, classid = NULL,
seqname = NULL, width.line = 60, lower.case = FALSE,
code.type = .code.type[1], sep = ""){
### matrix for aligned, list for unaligned.
if(!(is.vector(seqdata) || is.matrix(seqdata) || is.list(seqdata))){
stop("The seqdata should be a vector, matirx or list.")
}
if(is.null(code.type)){
code.type <- "UNKNOWN"
}
### transfer data.
if(code.type[1] == "NUCLEOTIDE"){
seqdata <- nid2code(seqdata, lower.case = lower.case)
} else if(code.type[1] == "SNP"){
seqdata <- sid2snp(seqdata)
} else if(code.type[1] == "CODON" && sep == ""){
sep <- ","
} else if(code.type[1] == "AMINO_ACID"){
seqdata <- aid2acode(seqdata, lower.case = lower.case)
}
ret <- write.fasta.format(seqdata, filename, classid = classid,
seqname = seqname, width.line = width.line,
sep = sep)
} # End of write.fasta().
write.phylip <- function(seqdata, filename, classid = NULL,
seqname = NULL, width.seqname = 10, width.line = 60, lower.case = FALSE,
code.type = .code.type[1], sep = ""){
# code.type = .code.type[1], sep = "", add.space = 10){
if(!(is.vector(seqdata) || is.matrix(seqdata)) || is.list(seqdata)){
stop("The seqdata should be a vector or matrix. (aligned)")
}
if(is.null(code.type)){
code.type <- "UNKNOWN"
}
### transfer data.
if(code.type[1] == "NUCLEOTIDE"){
seqdata <- nid2code(seqdata, lower.case = lower.case)
} else if(code.type[1] == "SNP"){
seqdata <- sid2snp(seqdata)
} else if(code.type[1] == "CODON" && sep == ""){
sep <- ","
} else if(code.type[1] == "AMINO_ACID"){
seqdata <- aid2acode(seqdata, lower.case = lower.case)
}
ret <- write.phylip.format(seqdata, filename, classid = classid,
seqname = seqname, width.seqname = width.seqname,
width.line = width.line, sep = sep)
# add.space = add.space)
} # End of write.phylip().
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