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\name{netToAxt}
\alias{netToAxt}
\title{
netToAxt
}
\description{
Wrapper function of \command{netToAxt} and \command{axtSort}:
convert net (and chain) to axt, and sort axt files.
This function doesn't work on the Windows platform since Kent utilities only
support Linux and Unix platforms.
}
\usage{
netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery,
axtFile=paste0(sub("\\\.2bit$", "", basename(assemblyTarget),
ignore.case = TRUE), ".",
sub("\\\.2bit$", "", basename(assemblyQuery),
ignore.case = TRUE), ".net.axt"),
removeFiles=FALSE,
binaryNetToAxt="netToAxt", binaryAxtSort="axtSort")
}
\arguments{
\item{in.net}{
\code{character}(1): file names of input \emph{net} file.
}
\item{in.chain}{
\code{character}(1): file names of input \emph{chain} file.
}
\item{assemblyTarget}{
\code{character}(1): the file name of target assembly \emph{twoBit} file.
}
\item{assemblyQuery}{
\code{character}(1): the file name of query assembly \emph{twoBit} file.
}
\item{axtFile}{
\code{character}(1): file names of output \emph{axt} file.
}
\item{removeFiles}{
\code{boolean}: When \code{TRUE}, the input \emph{net} and \emph{chain}
files will be removed after the conversion.
}
\item{binaryNetToAxt}{
\code{character}(1): the name/filename of the binary \command{netToAxt}
to call.
}
\item{binaryAxtSort}{
\code{character}(1): the name/filename of the binary \command{axtSort}
to call.
}
}
\value{
\code{character}(1): the file name of output \emph{axt} file.
}
\references{
\url{http://hgdownload.cse.ucsc.edu/admin/exe/}
}
\author{
Ge Tan
}
\seealso{
\code{\link{chainNetSyntenic}}
}
\examples{
\dontrun{
## This example doesn't run because it requires two bit files and external
## Kent utilities.
in.net <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
"danRer10.hg38.noClass.net")
in.chain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
"danRer10.hg38.all.pre.chain")
assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery,
axtFile=file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
paste0(sub("\\\.2bit$", "",
basename(assemblyTarget),
ignore.case = TRUE), ".",
sub("\\\.2bit$", "",
basename(assemblyQuery),
ignore.case = TRUE),
".net.axt")),
removeFiles=FALSE,
binaryNetToAxt="netToAxt", binaryAxtSort="axtSort")
}
}
|
