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substitutionrate.R
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substitutionrate.R
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#' @title Internal function for dNdS computations
#' @description This function takes a pairwise alignment as input file and estimates the
#' dNdS ratio of the corresponding alignment. Nevertheless, this function is a helper function for
#' \code{\link{dNdS}}. For dNdS computations you should use the function: \code{\link{dNdS}}.
#' @param file a character string specifying the path to a codon alignment file
#' @param est.method a character string specifying the dNdS estimation method, e.g. "Comeron","Li" .
#' Note, that when using "Comeron" as dNdS estimation method, the program 'gestimator' is used to compute the
#' corresponding dNdS values from a given alignment. The program 'gestimator' can only read "fasta" files,
#' hence it is important to use format = "fasta" when choosing est.method = "Comeron".
#' @param format a character string specifying the file format in which the alignment is stored:
#' "mase", "clustal", "phylip", "fasta" , "msf"
#' @param quiet a logical value specifying whether the output of the coresponding interface shall be printed out.
#' @param kaks_calc.params a character string storing additional parameters for KaKs_Claculator 1.2 . Default is \code{NULL}. Example:
#' \code{kaks_calc.params} = "-m NG -m YN".
#' @param kaks_calc_path a character string specifying the execution path to KaKs_Calculator. Default is \code{kaks_calc_path} = \code{NULL}
#' (meaning that KaKs_Calculator is stored and executable in your default \code{PATH}).
#' @param subst_name a character string specifying the substitution name that shall be added to the internal folder path naming.
#' Default is \code{subst_name} = \code{NULL}.
#' @author Hajk-Georg Drost and Sarah Scharfenberg
#' @details This function takes a pairwise alignments file as input and estimates dNdS ratios
#' of the corresponding alignments using predefined dNdS estimation methods.
#'
#' The dNdS estimation methods available in this function are:
#'
#' \itemize{
#' \item "Li" : Li's method (1993) -> provided by the ape package
#'
#' \item "Comeron" : Comeron's method (1995)
#' }
#' dNdS estimation methods provided by KaKs_Calculator 1.2 :
#'
#' Approximate Methods:
#'
#' \itemize{
#' \item "NG": Nei, M. and Gojobori, T. (1986)
#'
#' \item "LWL": Li, W.H., et al. (1985)
#'
#' \item "LPB": Li, W.H. (1993) and Pamilo, P. and Bianchi, N.O. (1993)
#'
#' \item "MLWL": (Modified LWL), MLPB (Modified LPB): Tzeng, Y.H., et al. (2004)
#'
#' \item "YN": Yang, Z. and Nielsen, R. (2000)
#'
#' \item "MYN": (Modified YN): Zhang, Z., et al. (2006)
#'
#' \item "GMYN": Wang, D.P., et al. Biology Direct. (2009)
#' \item "GY": Goldman, N. and Yang, Z. (1994)
#' \item "MS": (Model Selection)
#' \item "MA": (Model Averaging): based on a set of candidate models, Posada, D. (2003)
#' }
#'
#' Maximum-Likelihood Methods:
#' \itemize{
#' \item GY: Goldman, N. and Yang, Z. (1994)
#' }
#'
#' @examples \dontrun{
#'
#' # estimate the dNdS rate using Li's method
#' substitutionrate(
#' file = system.file("seqs/pal2nal.aln", package = "orthologr"),
#' est.method = "Li",
#' format = "fasta")
#'
#' # estimate the dNdS rate using Comeron's method
#' substitutionrate(
#' file = system.file("seqs/pal2nal.aln", package = "orthologr"),
#' est.method = "Comeron",
#' format = "fasta")
#'
#' # estimate the dNdS rate using model averaging provided by
#' # the KaKs_Calculator 1.2 program
#' substitutionrate(
#' file = system.file("seqs/pal2nal.aln", package = "orthologr"),
#' est.method = "MA",
#' format = "fasta")
#'
#' # estimate the dNdS rate using Nei and Gojobori's method provided by the
#' # KaKs_Calculator 1.2 program
#' substitutionrate(
#' file = system.file("seqs/pal2nal.aln", package = "orthologr"),
#' est.method = "NG",
#' format = "fasta")
#'
#' # estimate the dNdS rate using Nei and Gojobori's method AND Yang and Nielsen's
#' # method provided by the KaKs_Calculator 1.2 program
#' # for this purpose we choose:
#' # est.method = "kaks_calc" and kaks_calc.params = "-m NG -m YN"
#' substitutionrate(
#' file = system.file("seqs/pal2nal.aln", package = "orthologr"),
#' est.method = "kaks_calc",
#' format = "fasta",
#' kaks_calc.params = "-m NG -m YN")
#'
#'
#' }
#' @references
#' Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol., 36:96-99.
#'
#' Charif, D. and Lobry, J.R. (2007) SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.
#'
#' Thornton, K. (2003) libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17): 2325-2327
#'
#' Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs Calculator:
#' Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 2006 , 4:259-263.
#'
#' https://code.google.com/p/kaks-calculator/wiki/KaKs_Calculator
#'
#' https://code.google.com/p/kaks-calculator/wiki/AXT
#'
#' @return A data.table storing the query_id, subject_id, dN, dS, and dNdS values or
#' a data.table storing the query_id, method, dN, dS, and dNdS values when using KaKs_Calculator.
#' If the dNdS value cannot be calculated NA is returned. This can happen because of constraints
#' of the used model. As each program throws different exception values we set all of them to NA instead.
#' @seealso \code{\link{dNdS}}, \code{\link{multi_aln}}, \code{\link{codon_aln}}, \code{\link{blast_best}},
#' \code{\link{blast_rec}}, \code{\link{read.cds}}
#' @export
substitutionrate <- function(file,
est.method,
format = "fasta",
quiet = FALSE,
kaks_calc.params = NULL,
kaks_calc_path = NULL,
subst_name = NULL){
# dNdS estimation methods provided by the KaKs_Calculator program
kaks_calc_methods <-
c("MA",
"MS",
"NG",
"LWL",
"LPB",
"MLWL",
"YN",
"MYN",
"GY",
"GMYN",
"kaks_calc",
"ALL")
if (!is.dnds_est_method(est.method))
stop("Please choose a dNdS estimation method that is supported by this function.", call. = FALSE)
if (!is.element(format, c("mase", "clustal", "phylip", "fasta" , "msf")))
stop("Please choose a format that is supported by seqinr::read.alignment.", call. = FALSE)
# due to the discussion of no visible binding for global variable for
# data.table objects see:
# http://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check?lq=1
query_id <- dN <- dS <- NULL
# determine the file seperator of the current OS
f_sep <- .Platform$file.sep
if (!file.exists(file.path(tempdir(), "_calculation"))) {
dir.create(file.path(tempdir(), "_calculation"))
}
if (est.method == "Comeron") {
if (is.null(subst_name)) {
file.out <- file.path(tempdir(), "_calculation", "gestimout")
}
if (!is.null(subst_name)) {
file.out <-
file.path(tempdir(),
"_calculation",
paste0(subst_name, "_gestimout"))
}
# file in fasta required
if (format != "fasta")
stop("To use gestimator an alignment file in fasta format is required.")
tryCatch({
# To use gestimator a file in fasta format is required
# include this line instead of the following, to use internal gestimator
gestimator(file = file,
file_out = file.out)
#system(paste0("gestimator -i ",file," -o ",file.out))
hit.table <- data.table::fread(file.out)
data.table::setnames(
x = hit.table,
old = c("V1", "V2", "V3", "V4", "V5"),
new = c("query_id", "subject_id", "dN", "dS", "dNdS")
)
data.table::setkey(hit.table, query_id)
# for consistent output format we set the default value of gestimator 999
# to NA for output
# Therefor the user cannot make a mistake if using the dNdS results without
# filtering for some value.
hit.table[which(hit.table[, dS == 999]), dS := NA]
hit.table[which(hit.table[, dN == 999]), dN := NA]
hit.table[which(hit.table[, dNdS == 999]), dNdS := NA]
if (!quiet) {
message("Substitutionrate successfully calculated by gestimator.")
}
return(hit.table)
}, error = function(e) {
stop(
"Please check the correct path to ",
est.method,
"... the interface call did not work properly."
)
})
}
if (est.method == "Li") {
aln <- seqinr::read.alignment(file = file,
format = format)
res_list <- seqinr::kaks(aln)
res <-
data.table::data.table(t(c(
unlist(aln$nam),
res_list$ka,
res_list$ks,
(res_list$ka / res_list$ks)
)))
# seqinr::kaks documentation:
# When the alignment does not contain enough information (i.e we approach saturation),
# the Ka and Ks values take the value 10. Negative values indicate that Ka and Ks can
# not be computed.
# we set both of them to NA
data.table::setnames(
x = res,
old = paste0("V", 1:5),
new = c("query_id", "subject_id", "dN", "dS", "dNdS")
)
data.table::setkey(res, query_id)
res[which(res[, dN < 0]), dNdS := NA]
res[which(res[, dN < 0]), dN := NA]
res[which(res[, dS < 0]), dNdS := NA]
res[which(res[, dS < 0]), dS := NA]
res[which(res[, dN > 9.9]), dNdS := NA]
res[which(res[, dN > 9.9]), dN := NA]
res[which(res[, dS > 9.9]), dNdS := NA]
res[which(res[, dS > 9.9]), dS := NA]
if (!quiet) {
print("Substitutionrate successfully calculated using Li's method.")
}
return(res)
}
if (is.element(est.method, kaks_calc_methods)) {
is_installed_kaks_calculator()
operating_sys <- Sys.info()[1]
if (operating_sys == "Darwin") {
os <- "Mac"
calc <- "KaKs_Calculator"
}
if (operating_sys == "Linux") {
os <- "Linux"
calc <- "KaKs_Calculator"
}
if (operating_sys == "Windows") {
os <- "Windows"
calc <- "KaKs_Calculator.exe"
}
# determine the file seperator of the current OS
f_sep <- .Platform$file.sep
fa2axt <-
system.file(paste0("KaKs_Calc_parser", f_sep, "parseFastaIntoAXT.pl"),
package = "orthologr")
### replace paths like this: path/to a folder/of_interest
### by: path/'to a folder'/of_interest
file_name <- unlist(strsplit(file, f_sep))
file_name <- file_name[length(file_name)]
curr_wd <- unlist(strsplit(tempdir(), f_sep))
wdir <- grepl(" ", curr_wd)
if (any(wdir)) {
curr_wd[wdir] <- stringr::str_replace(
string = curr_wd[wdir],
replacement = paste0("'", curr_wd[wdir], "'"),
pattern = curr_wd[wdir]
)
}
curr_wd <- paste0(curr_wd, collapse = f_sep)
###
tryCatch({
# converting to input file for KaKs_Calculator
system(
paste0(
"perl ",
fa2axt ,
" ",
file,
" ",
curr_wd,
f_sep,
"_calculation",
f_sep,
file_name
)
)
# running KaKs_Calculator inside the orthologr package
# KaKs_Calculator <- system.file(paste0("KaKs_Calculator1.2",f_sep,"bin",f_sep,os,f_sep,calc), package = "orthologr")
if (is.null(kaks_calc_path))
KaKs_Calculator <- calc
if (!is.null(kaks_calc_path))
KaKs_Calculator <- paste0(kaks_calc_path, f_sep, calc)
if (is.null(kaks_calc.params)) {
system(paste0(
KaKs_Calculator,
" -i ",
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt")
),
" -o ",
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt.kaks")),
" -m ",
est.method
))
}
if (!is.null(kaks_calc.params)) {
system(paste0(
KaKs_Calculator,
" -i ",
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt")
),
" -o ",
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt.kaks")),
" ",
kaks_calc.params
))
}
}, error = function(e) {
stop(
"KaKs_Calculator couldn't run properly, please check your input files."
)
})
tryCatch({
kaks_tbl <-
utils::read.csv(
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt.kaks")
),
sep = "\t",
header = TRUE
)
kaks_tbl_res <- kaks_tbl[ , 1:5]
kaks_tbl_res <-
data.frame(
sapply(kaks_tbl_res[ , 1], function(x)
unlist(
strsplit(as.character(x), "-")
)[1]),
sapply(kaks_tbl_res[ , 1], function(x)
unlist(
strsplit(as.character(x), "-")
)[2]) ,
kaks_tbl_res[ , c(3:5, 2)]
)
names(kaks_tbl_res) <-
c("query_id",
"subject_id",
"dN",
"dS",
"dNdS",
"method")
kaks_tbl_res <- data.table::as.data.table(kaks_tbl_res)
data.table::setkey(kaks_tbl_res, query_id)
return(kaks_tbl_res)
}, error = function(e) {
stop(
"Something went wront with KaKs_Calculator.",
"\n",
file.path(
tempdir(),
"_calculation",
paste0(file_name, ".axt.kaks")
),
" could not be read properly."
)
})
}
}