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#This file is part of the source code for
#SPGS: an R package for identifying statistical patterns in genomic sequences.
#Copyright (C) 2015 Universidad de Chile and INRIA-Chile
#
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2 of the License, or
#(at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#GNU General Public License for more details.
#
#A copy of Version 2 of the GNU Public License is available in the
#share/licenses/gpl-2 file in the R installation directory or from
#http://www.R-project.org/Licenses/GPL-2.
#complement.R
complement <- function(x, ...)
UseMethod("complement")
complement.default <- function(x, content=c("dna", "rna"),
case=c("lower", "upper", "as is"), ...)
#returns the complement of the DNA or RNA sequences in x.
{
#Check arguments
if (!is.character(x)) x <- as.character(x) #coerse x to a character vector
content <- match.arg(content)
case <- match.arg(case)
if (length(x)==0 || (length(x)==1 && nchar(x)==0))
return(x) #bail if input is empty
if (case=="lower") x <- tolower(x)
if (case=="upper") x <- toupper(x)
if (content=="dna")
{
src <- "acgturykmswbdhvnxACGTURYKMSWBDHVNX-"
dest <- "tgcaayrmkswvhdbnxTGCAAyRMKSWVHDBNX-"
}
else
{
src <- "acgturykmswbdhvnxACGTURYKMSWBDHVNX-"
dest <- "ugcaayrmkswvhdbnxUGCAAyRMKSWVHDBNX-"
} #if
chartr(src, dest, x)
} #function
complement.SeqFastadna <- function(x, ...)
{
seq <- complement.default(as.character(x), ...)
attributes(seq) <- attributes(x)
seq
} #function
complement.list <- function(x, ...)
{
lapply(x, function(y) complement(y, ...))
} #function
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