| copySubstitute {Biobase} | R Documentation |
Copy files, directory trees or between connections and replace all occurences of a symbol by the corresponding value.
copySubstitute(src, dest, symbolValues, symbolDelimiter="@", allowUnresolvedSymbols=FALSE,
recursive = FALSE, removeExtension = "\\.in$")
src |
Source, either a character vector with filenames and/or directory names, or a connection object. |
dest |
Destination, either a character vector of length 1
with the name of an existing, writable directory, or a connection
object. The class of the |
symbolValues |
A named list of character strings. |
symbolDelimiter |
A character string of length one with a single character in it. |
allowUnresolvedSymbols |
Logical. If |
recursive |
Logical. If |
removeExtension |
Character. Matches to this regular expression are removed from filenames and directory names. |
Symbol substitution: this is best explained with an example. If the list
symbolValues contains an element with name FOO and value
bar, and symbolDelimiter is @, then any occurrence of
@FOO@ is replaced by bar. This applies both the text
contents of the files in src as well as to the filenames. See examples.
If recursive is FALSE, both src and dest
must be connection or a filenames. The text in src is read
through the function readLines,
symbols are replaced by their values, and the result is written to
dest through the function writeLines.
If recursive is TRUE,
copySubstitute
works recursively down a directory tree (see details and example).
src must be a character vector with multiple filenames or
directory names, dest a directory name.
One use of this function is in
createPackage
for the automatic generation of packages from a template package directory.
None. The function is called for its side effect.
Wolfgang Huber http://www.dkfz.de/mga/whuber
## create an example file
infile = tempfile()
outfile = tempfile()
writeLines(text=c("We will perform in @WHAT@:",
"So, thanks to @WHOM@ at once and to each one,",
"Whom we invite to see us crown'd at @WHERE@."),
con = infile)
## create the symbol table
z = list(WHAT="measure, time and place", WHOM="all", WHERE="Scone")
## run copySubstitute
copySubstitute(infile, outfile, z)
## display the results
readLines(outfile)
##--------------------------------------------------------------
## This is a slightly more complicated example that demonstrates
## how copySubstitute works on nested directories
##--------------------------------------------------------------
d = tempdir()
my.dir.create = function(x) {dir.create(x); return(x)}
unlink(file.path(d, "src"), recursive=TRUE)
unlink(file.path(d, "dest"), recursive=TRUE)
## create some directories and files:
src = my.dir.create(file.path(d, "src"))
dest = file.path(d, "dest")
d1 = my.dir.create(file.path(src, "dir1.in"))
d2 = my.dir.create(file.path(src, "dir2@FOO@.in"))
d3 = my.dir.create(file.path(d2, "dir3"))
d4 = my.dir.create(file.path(d3, "dir4"))
d5 = my.dir.create(file.path(d4, "dir5@BAR@"))
writeLines(c("File1:", "FOO: @FOO@"), file.path(d1, "file1.txt.in"))
writeLines(c("File2:", "BAR: @BAR@"), file.path(d2, "file2.txt.in"))
writeLines(c("File3:", "SUN: @SUN@"), file.path(d3, "file3.txt.in"))
writeLines(c("File4:", "MOON: @MOON@"), file.path(d4, "@SUN@.txt"))
## call copySubstitute
copySubstitute(src, dest, recursive=TRUE,
symbolValues = list(FOO="thefoo", BAR="thebar",
SUN="thesun", MOON="themoon"))
## view the result
listsrc = dir(src, full.names=TRUE, recursive=TRUE)
listdest = dir(dest, full.names=TRUE, recursive=TRUE)
listsrc
listdest
cat(unlist(lapply(listsrc, readLines)), sep="\n")
cat(unlist(lapply(listdest, readLines)), sep="\n")