R/multi_aln.R
In HajkD/orthologr: Comparative Genomics with R
Defines functions
multi_aln
Documented in
multi_aln
#' @title Compute Multiple Sequence Alignments
#' @description This function takes a FASTA file containing DNA or amino acid sequences
#' that shall be aligned and computes a multiple alignment using a defined multiple alignment tool.
#' @param file a character string specifying the path to the file storing the sequences in FASTA format.
#' @param tool a character string specifying the program that should be used: "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".
#' @param get_aln a logical value indicating whether the produced alignment should be returned.
#' @param path a character string specifying the path to the multiple alignment program (in case you don't use the default path).
#' @param multi_aln_name a character string specifying the name of the stored alignment file.
#' Default is \code{multi_aln_name} = \code{NULL} denoting a default name: 'toolname.aln' .
#' @param params a character string listing the input paramters that shall be passed to corresponding alignment tool specified in the \code{tool} argument.
#' Default is \code{NULL}, implicating that a set of default parameters is used when running the correponding tool, e.g. clustalw.
#' Example: \code{params} = "-PWMATRIX=BLOSUM -TYPE=PROTEIN" for \code{tool} = "clustalw.
#' @param quiet a logical value specifying whether the output of the corresponding multiple alignment tool shall be printed out to the console.
#' Default is \code{quiet} = \code{FALSE}.
#' @param clean_folders a boolean value spefiying whether all internall folders storing the output of used programs
#' shall be removed. Default is \code{clean_folders} = \code{FALSE}.
#' @author Hajk-Georg Drost and Sarah Scharfenberg
#' @details This function provides an interface between R and common multiple alignment programs
#' such as "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".
#'
#' \itemize{
#'
#' \item CLUSTALW :
#'
#'
#' Different operating systems perform different execution calls to the clustalw program:
#'
#' \itemize{
#' \item MacOS: 'clustalw2'
#' \item Linux: 'clustalw'
#' \item Windows: 'clustalw2.exe'
#' }
#'
#' In case you use the default path to the clustalw program, depending on your operating system,
#' the following calls to clustalw should work properly on your system:
#'
#' \itemize{
#' \item MacOS: \code{system("clustalw2 -help")}
#' \item Linux: \code{system("clustalw -help")}
#' \item Windows: \code{system("clustalw2.exe -help")}
#'
#' }
#'
#' In case these procedures don't work properly, please use the \code{path} argument
#' to specify the 'clustalw' execution path on your system:
#'
#' \itemize{
#' \item MacOS: \code{system("path/to/clustalw/clustalw2 -help")}
#' \item Linux: \code{system("path/to/clustalw/clustalw -help")}
#' \item Windows: \code{system("path/to/clustalw/clustalw2.exe -help")}
#'
#' }
#'
#' \item T_COFFEE :
#'
#' In case you use the default path to the t_coffee program,
#' the following calls to clustalw should work properly on your system:
#'
#' \code{system("t_coffee -version")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 't_coffee' execution path on your system:
#'
#' \code{system("path/to/t_coffee/t_coffee -version")}
#'
#'
#'
#' \item MUSCLE :
#'
#' In case you use the default path to the muscle program,
#' the following calls to muscle should work properly on your system:
#'
#' \code{system("muscle -help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'muscle' execution path on your system:
#'
#' \code{system("path/to/muscle/muscle -help")}
#'
#'
#' \item CLUSTALO :
#'
#' In case you use the default path to the clustalo program,
#' the following calls to clustalo should work properly on your system:
#'
#' \code{system("clustalo --help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'clustalo' execution path on your system:
#'
#' \code{system("path/to/clustalo/clustalo --help")}
#'
#'
#' \item MAFFT :
#'
#' In case you use the default path to the mafft program,
#' the following calls to mafft should work properly on your system:
#'
#' \code{system("mafft -help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'mafft' execution path on your system:
#'
#' \code{system("path/to/mafft/mafft -help")}
#'
#' }
#' @note Note that when using the \code{clustalw.params}, ... parameters, make sure the corresponding alignment tool
#' returns a file in clustal format *.aln. This is only important when \code{get_aln} = \code{TRUE}.
#' @examples \dontrun{
#'
#' # CLUSTALW Example:
#'
#' # in case the default execution path of clustalw runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE)
#'
#' # in case the default execution path of clustalw is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE,
#' path = "path/to/clustalw/")
#'
#' # running clustalw using additional parameters
#' # details: system("clustalw2 -help")
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE,
#' params = "-PWMATRIX=BLOSUM -TYPE=PROTEIN")
#'
#'
#' # T_COFFEE Example:
#'
#' # in case the default execution path of t_coffee runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE)
#'
#' # in case the default execution path of t_coffee is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE,
#' path = "path/to/t_coffee/")
#'
#' # running t_coffee using additional parameters
#' # details: http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE,
#' params = "-mode expresso")
#'
#'
#'
#' # MUSCLE Example:
#'
#' # in case the default execution path of muscle runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE)
#'
#' # in case the default execution path of muscle is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE,
#' path = "path/to/muscle/")
#'
#' # running muscle using additional parameters
#' # details: http://www.drive5.com/muscle/manual/
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE,
#' params = "-diags -clwstrict")
#'
#'
#' # CLUSTALO Example:
#'
#' # in case the default execution path of clustalo runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE)
#'
#' # in case the default execution path of clustalo is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE,
#' path = "path/to/clustalo/")
#'
#' # running clustalo using additional parameters
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE,
#' params = "--outfmt clu")
#'
#'
#'
#' # MAFFT Example:
#'
#' # in case the default execution path of mafft runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE)
#'
#' # in case the default execution path of mafft is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE,
#' path = "path/to/mafft/")
#'
#' # running mafft using additional parameters
#' # details: http://www.drive5.com/mafft/manual/
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE,
#' params = "--maxiterate 1 --clustalout")
#'
#'
#' }
#' @references
#'
#' \itemize{
#' \item CLUSTALW:
#'
#' Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F,
#' Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007).
#' Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
#'
#' \url{http://www.clustal.org/clustal2/}
#'
#' \url{http://www.ebi.ac.uk/Tools/msa/clustalw2/help/}
#'
#'
#' \item T_COFFEE
#'
#' T-Coffee: A novel method for multiple sequence alignments.
#' Notredame, Higgins, Heringa, JMB, 302(205-217). 2000.
#'
#' \url{http://www.tcoffee.org/Projects/tcoffee/}
#'
#' \url{http://www.tcoffee.org/Projects/tcoffee/documentation/t_coffee_tutorial.pdf}
#'
#'
#' \item MUSCLE:
#'
#' Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.
#'
#' Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113.
#'
#' \url{http://www.drive5.com/muscle/}
#'
#' \url{http://www.drive5.com/muscle/manual/}
#'
#'
#' \item CLUSTALO:
#'
#' Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soeding J, Thompson JD, Higgins DG (2011).
#' Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
#'
#' \url{http://www.clustal.org/omega/}
#'
#' \url{http://www.clustal.org/omega/README}
#'
#' \item MAFFT :
#'
#' Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780)
#' MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
#'
#' \url{http://mafft.cbrc.jp/alignment/software/}
#'
#' \url{http://mafft.cbrc.jp/alignment/software/manual/manual.html}
#'
#' \url{http://mafft.cbrc.jp/alignment/software/tips0.html}
#'
#' }
#' @return In case the argument \code{get_aln} is set \code{TRUE}, an object of class alignment of the seqinr package is returned.
#' @export
multi_aln <- function(file,
tool,
get_aln = FALSE,
path = NULL,
multi_aln_name = NULL,
params = NULL,
quiet = FALSE,
clean_folders = FALSE){
if(!is.multiple_aln_tool(tool))
stop("Please choose a tool that is supported by this function.")
if (!file.exists(file.path(tempdir(), "_alignment"))) {
dir.create(file.path(tempdir(), "_alignment"))
}
if (!file.exists(file.path(tempdir(), "_alignment", "multi_aln"))) {
dir.create(file.path(tempdir(), "_alignment", "multi_aln"))
}
if (is.null(multi_aln_name)) {
file.out <-
file.path(tempdir(),
"_alignment",
"multi_aln",
paste0(basename(file), "_", tool, ".aln"))
}
if (!is.null(multi_aln_name)) {
file.out <-
file.path(
tempdir(),
"_alignment",
"multi_aln",
paste0(multi_aln_name, "_", tool, ".aln")
)
}
# does not work as expected, could be included in another way or not.
# if(quiet){
# clustalw.params = paste0(clustalw.params, " -QUIET")
# mafft.params = paste0(mafft.params, " --quiet")
# muscle.params = paste0(muscle.params, " -quiet")
# # clustalo - no param found to limit the output
# }
# RIGHT NOW EACH NEW RUN OF THE FUNCTION OVERWRITES
# THE EXISTING *.aln FILE
# IN FUTURE VERSIONS WE SHOULD TRY TO KEEP (STORE) EXISTING FILES
# AND RENAME THE NEW ONES
if (tool == "clustalw") {
is_installed_clustalw()
# find out on what kind of OS ClustalW is running
operating_sys <- Sys.info()[1]
if (operating_sys == "Darwin")
call_clustalw <- "clustalw2"
if (operating_sys == "Linux")
call_clustalw <- "clustalw2"
if (operating_sys == "Windows")
call_clustalw <- "clustalw2.exe"
# test whether the connection to clustalw works
tryCatch({
if (is.null(path)) {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# There is an error with pal2nal as clustalw deletes * during alignment what results in
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# right now only the default parameters for args: "-PWGAPOPEN", "-PWGAPEXT", "-GAPOPEN", "-GAPEXT" are being used
system(
paste0(
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" -quiet"
)
)
} else {
# add additional parameters when running clustalw
system(
paste0(
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" ",
params
)
)
}
} else {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running clustalw
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" -quiet"
)
)
} else {
# add additional parameters when running clustalw
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" ",
params
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "t_coffee") {
is_installed_tcoffee()
# test whether the connection to t_coffee works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# There is an error with pal2nal as t_coffee deletes * during alignment what results in
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# use the default parameters when running t_coffee
# perform an accurate alignment which is very accurate, but slow
# http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
system(
paste0(
"t_coffee -infile ",
file,
" -mode accurate",
" -outfile ",
file.out
)
)
} else {
# add additional parameters when running t_coffee
system(
paste0(
"t_coffee -infile ",
file,
" ",
params,
" -outfile ",
file.out
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running t_coffee
# perform a accurate alignment which is very accurate, but slow
# http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"t_coffee -infile ",
file,
" -mode accurate",
" -outfile ",
file.out
)
)
} else {
# add additional parameters when running t_coffee
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"t_coffee -infile ",
file,
" ",
params,
" -outfile ",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function() {
stop(
paste0(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "muscle") {
is_installed_muscle()
# test whether the connection to muscle works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# There is an error with pal2nal as muscle deletes * during alignment what results in
# muscle: *** WARNING *** Invalid character '*' in FASTA sequence data, ignored
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# use the default parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"muscle -in ",
file,
" -out ",
file.out,
" -clwstrict",
" -quiet"
)
)
} else {
# add additional parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"muscle -in ",
file,
" ",
params,
" -out ",
file.out
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"muscle -in ",
file,
" -out ",
file.out,
" -clwstrict",
" -quiet"
)
)
} else {
# add additional parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"muscle -in ",
file,
" ",
params,
" -out ",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "clustalo") {
is_installed_clustalo()
# test whether the connection to clustalo works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# use the default parameters when running clustalo
system(
paste0(
"clustalo -i ",
file,
" -o ",
file.out,
" --outfmt clu --force"
)
)
} else {
# add additional parameters when running clustalo
system(
paste0(
"clustalo -i ",
file,
" -o ",
file.out,
" --force ",
params
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running clustalo
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"clustalo -i ",
file,
" -o ",
file.out,
" --outfmt clustal --force"
)
)
} else {
# add additional parameters when running clustalo
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"clustalo -i ",
file,
" -o ",
file.out,
" --force ",
params
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "mafft") {
is_installed_mafft()
# test whether the connection to mafft works
tryCatch({
if (is.null(path)) {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running mafft
system(
paste0(
"mafft --quiet --anysymbol --clustalout ",
file,
" >",
file.out
)
)
# To avoid error with pal2nal when deleting * during multiple
# alignment add --anysymbol
# http://mbe.oxfordjournals.org/content/early/2013/02/08/molbev.mst010.full
} else {
# add additional parameters when running mafft
system(paste0(
"mafft ",
params,
" ",
file,
" >",
file.out
))
}
} else {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running mafft
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"mafft --quiet --anysymbol --clustalout ",
file,
" >",
file.out
)
)
} else {
# add additional parameters when running mafft
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"mafft",
" ",
params,
" ",
file,
" >",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
## LINUX ERROR
# There is a problem in the configuration of your shell.
# Check the MAFFT_BINARIES environmental variable by
# $ echo $MAFFT_BINARIES
# This variable must be *unset*, unless you have installed MAFFT
# with a special configuration. To unset this variable, type
# $ unset MAFFT_BINARIES or $ unsetenv MAFFT_BINARIES
# To keep this change permanently, edit setting files
# (.bash_profile, .profile, .cshrc, etc) in your home directory
# to delete the MAFFT_BINARIES line.
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (clean_folders)
clean_all_folders(file.path(tempdir(), "_alignment")
)
}
HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.
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Defines functions multi_aln
Documented in multi_aln
#' @title Compute Multiple Sequence Alignments
#' @description This function takes a FASTA file containing DNA or amino acid sequences
#' that shall be aligned and computes a multiple alignment using a defined multiple alignment tool.
#' @param file a character string specifying the path to the file storing the sequences in FASTA format.
#' @param tool a character string specifying the program that should be used: "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".
#' @param get_aln a logical value indicating whether the produced alignment should be returned.
#' @param path a character string specifying the path to the multiple alignment program (in case you don't use the default path).
#' @param multi_aln_name a character string specifying the name of the stored alignment file.
#' Default is \code{multi_aln_name} = \code{NULL} denoting a default name: 'toolname.aln' .
#' @param params a character string listing the input paramters that shall be passed to corresponding alignment tool specified in the \code{tool} argument.
#' Default is \code{NULL}, implicating that a set of default parameters is used when running the correponding tool, e.g. clustalw.
#' Example: \code{params} = "-PWMATRIX=BLOSUM -TYPE=PROTEIN" for \code{tool} = "clustalw.
#' @param quiet a logical value specifying whether the output of the corresponding multiple alignment tool shall be printed out to the console.
#' Default is \code{quiet} = \code{FALSE}.
#' @param clean_folders a boolean value spefiying whether all internall folders storing the output of used programs
#' shall be removed. Default is \code{clean_folders} = \code{FALSE}.
#' @author Hajk-Georg Drost and Sarah Scharfenberg
#' @details This function provides an interface between R and common multiple alignment programs
#' such as "clustalw", "t_coffee", "muscle", "clustalo", and "mafft".
#'
#' \itemize{
#'
#' \item CLUSTALW :
#'
#'
#' Different operating systems perform different execution calls to the clustalw program:
#'
#' \itemize{
#' \item MacOS: 'clustalw2'
#' \item Linux: 'clustalw'
#' \item Windows: 'clustalw2.exe'
#' }
#'
#' In case you use the default path to the clustalw program, depending on your operating system,
#' the following calls to clustalw should work properly on your system:
#'
#' \itemize{
#' \item MacOS: \code{system("clustalw2 -help")}
#' \item Linux: \code{system("clustalw -help")}
#' \item Windows: \code{system("clustalw2.exe -help")}
#'
#' }
#'
#' In case these procedures don't work properly, please use the \code{path} argument
#' to specify the 'clustalw' execution path on your system:
#'
#' \itemize{
#' \item MacOS: \code{system("path/to/clustalw/clustalw2 -help")}
#' \item Linux: \code{system("path/to/clustalw/clustalw -help")}
#' \item Windows: \code{system("path/to/clustalw/clustalw2.exe -help")}
#'
#' }
#'
#' \item T_COFFEE :
#'
#' In case you use the default path to the t_coffee program,
#' the following calls to clustalw should work properly on your system:
#'
#' \code{system("t_coffee -version")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 't_coffee' execution path on your system:
#'
#' \code{system("path/to/t_coffee/t_coffee -version")}
#'
#'
#'
#' \item MUSCLE :
#'
#' In case you use the default path to the muscle program,
#' the following calls to muscle should work properly on your system:
#'
#' \code{system("muscle -help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'muscle' execution path on your system:
#'
#' \code{system("path/to/muscle/muscle -help")}
#'
#'
#' \item CLUSTALO :
#'
#' In case you use the default path to the clustalo program,
#' the following calls to clustalo should work properly on your system:
#'
#' \code{system("clustalo --help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'clustalo' execution path on your system:
#'
#' \code{system("path/to/clustalo/clustalo --help")}
#'
#'
#' \item MAFFT :
#'
#' In case you use the default path to the mafft program,
#' the following calls to mafft should work properly on your system:
#'
#' \code{system("mafft -help")}
#'
#' In case this procedures doesn't work properly, please use the \code{path} argument
#' to specify the 'mafft' execution path on your system:
#'
#' \code{system("path/to/mafft/mafft -help")}
#'
#' }
#' @note Note that when using the \code{clustalw.params}, ... parameters, make sure the corresponding alignment tool
#' returns a file in clustal format *.aln. This is only important when \code{get_aln} = \code{TRUE}.
#' @examples \dontrun{
#'
#' # CLUSTALW Example:
#'
#' # in case the default execution path of clustalw runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE)
#'
#' # in case the default execution path of clustalw is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE,
#' path = "path/to/clustalw/")
#'
#' # running clustalw using additional parameters
#' # details: system("clustalw2 -help")
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalw",
#' get_aln = TRUE,
#' params = "-PWMATRIX=BLOSUM -TYPE=PROTEIN")
#'
#'
#' # T_COFFEE Example:
#'
#' # in case the default execution path of t_coffee runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE)
#'
#' # in case the default execution path of t_coffee is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE,
#' path = "path/to/t_coffee/")
#'
#' # running t_coffee using additional parameters
#' # details: http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "t_coffee",
#' get_aln = TRUE,
#' params = "-mode expresso")
#'
#'
#'
#' # MUSCLE Example:
#'
#' # in case the default execution path of muscle runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE)
#'
#' # in case the default execution path of muscle is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE,
#' path = "path/to/muscle/")
#'
#' # running muscle using additional parameters
#' # details: http://www.drive5.com/muscle/manual/
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "muscle",
#' get_aln = TRUE,
#' params = "-diags -clwstrict")
#'
#'
#' # CLUSTALO Example:
#'
#' # in case the default execution path of clustalo runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE)
#'
#' # in case the default execution path of clustalo is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE,
#' path = "path/to/clustalo/")
#'
#' # running clustalo using additional parameters
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "clustalo",
#' get_aln = TRUE,
#' params = "--outfmt clu")
#'
#'
#'
#' # MAFFT Example:
#'
#' # in case the default execution path of mafft runs properly on your system
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE)
#'
#' # in case the default execution path of mafft is not set within the default path
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE,
#' path = "path/to/mafft/")
#'
#' # running mafft using additional parameters
#' # details: http://www.drive5.com/mafft/manual/
#' multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
#' tool = "mafft",
#' get_aln = TRUE,
#' params = "--maxiterate 1 --clustalout")
#'
#'
#' }
#' @references
#'
#' \itemize{
#' \item CLUSTALW:
#'
#' Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F,
#' Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007).
#' Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
#'
#' \url{http://www.clustal.org/clustal2/}
#'
#' \url{http://www.ebi.ac.uk/Tools/msa/clustalw2/help/}
#'
#'
#' \item T_COFFEE
#'
#' T-Coffee: A novel method for multiple sequence alignments.
#' Notredame, Higgins, Heringa, JMB, 302(205-217). 2000.
#'
#' \url{http://www.tcoffee.org/Projects/tcoffee/}
#'
#' \url{http://www.tcoffee.org/Projects/tcoffee/documentation/t_coffee_tutorial.pdf}
#'
#'
#' \item MUSCLE:
#'
#' Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797.
#'
#' Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, (5) 113.
#'
#' \url{http://www.drive5.com/muscle/}
#'
#' \url{http://www.drive5.com/muscle/manual/}
#'
#'
#' \item CLUSTALO:
#'
#' Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soeding J, Thompson JD, Higgins DG (2011).
#' Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75
#'
#' \url{http://www.clustal.org/omega/}
#'
#' \url{http://www.clustal.org/omega/README}
#'
#' \item MAFFT :
#'
#' Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780)
#' MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
#'
#' \url{http://mafft.cbrc.jp/alignment/software/}
#'
#' \url{http://mafft.cbrc.jp/alignment/software/manual/manual.html}
#'
#' \url{http://mafft.cbrc.jp/alignment/software/tips0.html}
#'
#' }
#' @return In case the argument \code{get_aln} is set \code{TRUE}, an object of class alignment of the seqinr package is returned.
#' @export
multi_aln <- function(file,
tool,
get_aln = FALSE,
path = NULL,
multi_aln_name = NULL,
params = NULL,
quiet = FALSE,
clean_folders = FALSE){
if(!is.multiple_aln_tool(tool))
stop("Please choose a tool that is supported by this function.")
if (!file.exists(file.path(tempdir(), "_alignment"))) {
dir.create(file.path(tempdir(), "_alignment"))
}
if (!file.exists(file.path(tempdir(), "_alignment", "multi_aln"))) {
dir.create(file.path(tempdir(), "_alignment", "multi_aln"))
}
if (is.null(multi_aln_name)) {
file.out <-
file.path(tempdir(),
"_alignment",
"multi_aln",
paste0(basename(file), "_", tool, ".aln"))
}
if (!is.null(multi_aln_name)) {
file.out <-
file.path(
tempdir(),
"_alignment",
"multi_aln",
paste0(multi_aln_name, "_", tool, ".aln")
)
}
# does not work as expected, could be included in another way or not.
# if(quiet){
# clustalw.params = paste0(clustalw.params, " -QUIET")
# mafft.params = paste0(mafft.params, " --quiet")
# muscle.params = paste0(muscle.params, " -quiet")
# # clustalo - no param found to limit the output
# }
# RIGHT NOW EACH NEW RUN OF THE FUNCTION OVERWRITES
# THE EXISTING *.aln FILE
# IN FUTURE VERSIONS WE SHOULD TRY TO KEEP (STORE) EXISTING FILES
# AND RENAME THE NEW ONES
if (tool == "clustalw") {
is_installed_clustalw()
# find out on what kind of OS ClustalW is running
operating_sys <- Sys.info()[1]
if (operating_sys == "Darwin")
call_clustalw <- "clustalw2"
if (operating_sys == "Linux")
call_clustalw <- "clustalw2"
if (operating_sys == "Windows")
call_clustalw <- "clustalw2.exe"
# test whether the connection to clustalw works
tryCatch({
if (is.null(path)) {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# There is an error with pal2nal as clustalw deletes * during alignment what results in
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# right now only the default parameters for args: "-PWGAPOPEN", "-PWGAPEXT", "-GAPOPEN", "-GAPEXT" are being used
system(
paste0(
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" -quiet"
)
)
} else {
# add additional parameters when running clustalw
system(
paste0(
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" ",
params
)
)
}
} else {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running clustalw
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" -quiet"
)
)
} else {
# add additional parameters when running clustalw
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
call_clustalw,
" -infile=",
file,
" -outfile=",
file.out,
" ",
params
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "t_coffee") {
is_installed_tcoffee()
# test whether the connection to t_coffee works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# There is an error with pal2nal as t_coffee deletes * during alignment what results in
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# use the default parameters when running t_coffee
# perform an accurate alignment which is very accurate, but slow
# http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
system(
paste0(
"t_coffee -infile ",
file,
" -mode accurate",
" -outfile ",
file.out
)
)
} else {
# add additional parameters when running t_coffee
system(
paste0(
"t_coffee -infile ",
file,
" ",
params,
" -outfile ",
file.out
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running t_coffee
# perform a accurate alignment which is very accurate, but slow
# http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"t_coffee -infile ",
file,
" -mode accurate",
" -outfile ",
file.out
)
)
} else {
# add additional parameters when running t_coffee
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"t_coffee -infile ",
file,
" ",
params,
" -outfile ",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function() {
stop(
paste0(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "muscle") {
is_installed_muscle()
# test whether the connection to muscle works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# There is an error with pal2nal as muscle deletes * during alignment what results in
# muscle: *** WARNING *** Invalid character '*' in FASTA sequence data, ignored
# pal2nal: #--- ERROR: inconsistency between the following pep and nuc seqs ---#
# use the default parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"muscle -in ",
file,
" -out ",
file.out,
" -clwstrict",
" -quiet"
)
)
} else {
# add additional parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"muscle -in ",
file,
" ",
params,
" -out ",
file.out
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"muscle -in ",
file,
" -out ",
file.out,
" -clwstrict",
" -quiet"
)
)
} else {
# add additional parameters when running muscle
# write output into clustalw format using the -clwstrict argument
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"muscle -in ",
file,
" ",
params,
" -out ",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "clustalo") {
is_installed_clustalo()
# test whether the connection to clustalo works
tryCatch({
if (is.null(path)) {
if (is.null(params)) {
# use the default parameters when running clustalo
system(
paste0(
"clustalo -i ",
file,
" -o ",
file.out,
" --outfmt clu --force"
)
)
} else {
# add additional parameters when running clustalo
system(
paste0(
"clustalo -i ",
file,
" -o ",
file.out,
" --force ",
params
)
)
}
} else {
if (is.null(params)) {
# use the default parameters when running clustalo
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"clustalo -i ",
file,
" -o ",
file.out,
" --outfmt clustal --force"
)
)
} else {
# add additional parameters when running clustalo
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"clustalo -i ",
file,
" -o ",
file.out,
" --force ",
params
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (tool == "mafft") {
is_installed_mafft()
# test whether the connection to mafft works
tryCatch({
if (is.null(path)) {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running mafft
system(
paste0(
"mafft --quiet --anysymbol --clustalout ",
file,
" >",
file.out
)
)
# To avoid error with pal2nal when deleting * during multiple
# alignment add --anysymbol
# http://mbe.oxfordjournals.org/content/early/2013/02/08/molbev.mst010.full
} else {
# add additional parameters when running mafft
system(paste0(
"mafft ",
params,
" ",
file,
" >",
file.out
))
}
} else {
# if no specific parameters are set,
# then use the default parameters
if (is.null(params)) {
# use the default parameters when running mafft
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"mafft --quiet --anysymbol --clustalout ",
file,
" >",
file.out
)
)
} else {
# add additional parameters when running mafft
system(
paste0(
"export PATH=$PATH:",
path,
"; ",
"mafft",
" ",
params,
" ",
file,
" >",
file.out
)
)
}
}
if (!quiet) {
print(
paste0(
"Multiple Alignment successfully written in ",
file.out,
"."
)
)
}
}, error = function(e) {
stop(
"Please check the correct path to ",
tool,
"... the interface call did not work properly."
)
})
## LINUX ERROR
# There is a problem in the configuration of your shell.
# Check the MAFFT_BINARIES environmental variable by
# $ echo $MAFFT_BINARIES
# This variable must be *unset*, unless you have installed MAFFT
# with a special configuration. To unset this variable, type
# $ unset MAFFT_BINARIES or $ unsetenv MAFFT_BINARIES
# To keep this change permanently, edit setting files
# (.bash_profile, .profile, .cshrc, etc) in your home directory
# to delete the MAFFT_BINARIES line.
if (get_aln) {
tryCatch({
aln <-
Biostrings::readAAMultipleAlignment(file.out, format = "clustal")
return(aln)
}, error = function(e) {
stop(
"Something went wront with ",
tool,
" .",
"\n",
file.out,
" could not be read properly."
)
})
}
}
if (clean_folders)
clean_all_folders(file.path(tempdir(), "_alignment")
)
}
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