I have a directory which has 5 files named like this
A.abcd (1).txt
B.abcd (1).txt
C.abcd (1).txt
D.abcd (1).txt
E.abcd (1).txt
I want to change the names of the file so that they should become like this :
A.defg.txt
B.defg.txt
C.defg.txt
D.defg.txt
E.defg.txt
In short I want to change abcd (1) to defg in the files.
I tried to run the system command from the R console.
system("mv A.abcd (1).txt A.defg.txt")
But I have to do this one by one.
Is there any way I can do it in one shot through R ??
You can use file.rename() to rename files. And use sub with a regular expression for the text manipulation.
x <- c("A.abcd (1).txt", "B.abcd (1).txt", "C.abcd (1).txt", "D.abcd (1).txt", "E.abcd (1).txt")
newx <- sub("abcd \\(1\\)", "defg", x)
newx
[1] "A.defg.txt" "B.defg.txt" "C.defg.txt" "D.defg.txt" "E.defg.txt"
## The following is untested
file.rename(x, newx)
See ?files for help on this and the other base R file manipulation functions.
Related
I have two files with one being text, and the other being a data frame, now I just want to merge them into one as a text file. With linux, I can use:
cat file1 file2 > outputfile
I wonder if we can do the same thing with R?
file1
##TITLE=POOLED SAMPLES COLLECTED 05-06/03/2018
##JCAMP-DX=4.24
##DATA TYPE=LINK
#ORIGIN Bentley_FTS SomaCount_FCM 82048
##OWNER=Bentley Instruments Inc
##DATE=2018-03-09
##TIME=15:34:48
##BLOCKS=110
##LAB1=Auto Generated
##LAB2=
##CHANNELNAMES=8
file 2:
649.025085449219 0.063037105 0.021338785 -0.00053594 0.008937807 0.03266982
667.675231457819 0.028557044 0.005877694 -0.015043681 0.014945094 0.051547796
686.325377466418 0.021499421 0.017125281 0.043007832 0.04132269 0.027496092
704.975523475018 0.006128653 -0.014599532 -0.000335723 0.020189898 0.024547976
723.625669483618 0.018550962 0.018567896 0.014100821 0.013067127 0.027075281
742.275815492218 0.030145327 0.039745297 0.050556265 0.056621946 0.058416516
760.925961500818 0.040279277 0.01392867 -0.00143011 0.015103153 0.03580305
779.576107509418 0.031955898 0.013671243 0.000861743 0.000641993 0.001747168
Thanks alot
Phuong
We can use file.append:
file.append("fileMerged.txt", "file1.txt")
file.append("fileMerged.txt", "file2.txt")
Or if files are already imported into R, then write with append:
#import to R
f1 <- readLines("file1.txt")
f2 <- readLines("file2.txt")
# output with append
write(f1, "fileMerged.txt")
write(f2, "fileMerged.txt", append = TRUE)
I try to make it simple. I've got in my working directory "Laurent/R" csv files (never more than 5) with names that change from one experiment to the other.
Is it possible to use for and if loops to display each file one after the other and ask for each of them: "is it a "control" file ?", or to ask for each file something like " Is " "file.name[i] " "a control file ? " and codify the answer for the next steps ?
Thanks
I think you're looking for something like this:
label_controls <- function(my_dir)
{
filenames <- list.files(my_dir)
is_control <- logical(length(filenames))
for(i in seq_along(filenames))
{
cat(filenames[i], "\n")
answer <- readline("Is this a control file (Y/N)? : ")
is_control[i] <- grepl("Y|y", answer)
cat("\n")
}
data.frame(filenames, is_control)
}
If you run this function with a particular directory, it will prompt you for each file whether it is a control file or not, to which you answer Y or N. It will return a data frame of all the files in the directory in one column, with a second column indicating whether that file is a control file or not:
df <- label_controls("Me/Subdir/files")
my_csv1.csv
Is this a control file (Y/N)? : N
my_csv2.csv
Is this a control file (Y/N)? : Y
my_csv3.csv
Is this a control file (Y/N)? : N
And you can review the results:
df
#> filenames is_control
#> 1 my_csv1.csv FALSE
#> 2 my_csv2.csv TRUE
#> 3 my_csv3.csv FALSE
I am integrating an R script to produce some graphics into a larger project that is pulled together with a Makefile. In this larger project, I have a file called globals.mk that contains global variables used by many other scripts in the project. For example, the number of simulations I want to run is a global that I want to use in this R script. Can I "import" this as a variable, or is it necessary to manually define every variable within the R script?
Edit: here is a sample of the globals that I would need to read in.
num = 100
path = ./here/is/a/path
file = $(path)/file.csv
And I would like the R script to set the variables num as 100 (or "100"), path as "./here/is/a/path" and file as "./here/is/a/path/file.csv".
If it is ok to replace the parentheses with brace brackets then readRenviron will read in such files and perform the substitutions returning the contents as environmental variables.
# write out test file globals2.mk which uses brace brackets
Lines <- "num = 100
path = ./here/is/a/path
file = ${path}/file.csv"
cat(Lines, file = "globals2.mk")
readRenviron("globals2.mk")
Sys.getenv("num")
## [1] "100"
Sys.getenv("path")
## [1] "./here/is/a/path"
Sys.getenv("file")
## [1] "./here/is/a/path/file.csv"
If it is important to use parentheses rather than brace brackets, read in globals.mk, replace the parentheses with brace brackets and then write the file out again.
# write out test file - this one uses parentheses as in question
Lines <- "num = 100
path = ./here/is/a/path
file = $(path)/file.csv"
cat(Lines, file = "globals.mk")
# read globals.mk, perform () to {} substitutions, write out and then re-read
tmp <- tempfile()
L <- readLines("globals.mk")
cat(paste(chartr("()", "{}", L), collapse = "\n"), file = tmp)
readRenviron(tmp)
If the .mk file has anything other than direct variable expansion (such as more complex make-rules/tricks/functions), it might be better to trust make to do the expansion for you, and then read it in. There's a post here that I found that dumps all variable contents (after processing).
TL;DR
expand_mkvars <- function(path, aslist = FALSE) {
stopifnot(file.exists(mk <- Sys.which("make")))
tf <- tempfile(fileext = ".mk")
# needed on my windows system
tf <- normalizePath(tf, winslash = "/", mustWork = FALSE) # tempfile should suffice
on.exit(suppressWarnings(file.remove(tf)), add = TRUE)
writeLines(c(".PHONY: printvars",
"printvars:",
"\t#$(foreach V,$(sort $(.VARIABLES)), \\",
"\t $(if $(filter-out environment% default automatic, \\",
"\t $(origin $V)),$(warning $V=$($V))))"), con = tf)
out <- system2(mk, c("-f", shQuote(path), "-f", shQuote(tf), "-n", "printvars"),
stdout = TRUE, stderr = TRUE)
out <- out[grepl(paste0("^", tf), out)]
out <- gsub(paste0("^", tf, ":[0-9]+:\\s*"), "", out)
known_noneed <- c(".DEFAULT_GOAL", "CURDIR", "GNUMAKEFLAGS", "MAKEFILE_LIST", "MAKEFLAGS")
out <- out[!grepl(paste0("^(", paste(known_noneed, collapse = "|"), ")="), out)]
if (aslist) {
spl <- strsplit(out, "=")
nms <- sapply(spl, `[[`, 1)
rest <- lapply(spl, function(a) paste(a[-1], collapse = "="))
setNames(rest, nms)
} else out
}
In action:
expand_mkvars("~/StackOverflow/karthikt.mk")
# [1] "file=./here/is/a/path/file.csv" "num=100"
# [3] "path=./here/is/a/path"
expand_mkvars("~/StackOverflow/karthikt.mk", aslist = TRUE)
# $file
# [1] "./here/is/a/path/file.csv"
# $num
# [1] "100"
# $path
# [1] "./here/is/a/path"
I have not tested on other systems, so you might need to adjust known_noneed to add extra variables that popup. Depending on your needs, you might be able to filter more-intelligently (e.g., none of your variables lead with a capital letter), but for this example I kept it to the known-not-wanted variables that make is giving us.
The blog post suggests using a phony target of
.PHONY: printvars
printvars:
#$(foreach V,$(sort $(.VARIABLES)), \
$(if $(filter-out environment% default automatic, \
$(origin $V)),$(warning $V=$($V))))
(some are tabs, not all spaces, very important for make)
Unfortunately, it produces more output than you technically need:
$ /c/Rtools/bin/make.exe -f ~/StackOverflow/karthikt.mk printvars
C:/Users/r2/StackOverflow/karthikt.mk:10: .DEFAULT_GOAL=all
C:/Users/r2/StackOverflow/karthikt.mk:10: CURDIR=/Users/r2/Projects/Ford/shiny/shinyobjects/inst
C:/Users/r2/StackOverflow/karthikt.mk:10: GNUMAKEFLAGS=
C:/Users/r2/StackOverflow/karthikt.mk:10: MAKEFILE_LIST= C:/Users/r2/StackOverflow/karthikt.mk
C:/Users/r2/StackOverflow/karthikt.mk:10: MAKEFLAGS=
C:/Users/r2/StackOverflow/karthikt.mk:10: SHELL=sh
C:/Users/r2/StackOverflow/karthikt.mk:10: file=./here/is/a/path/file.csv
C:/Users/r2/StackOverflow/karthikt.mk:10: num=100
C:/Users/r2/StackOverflow/karthikt.mk:10: path=./here/is/a/path
make: Nothing to be done for 'printvars'.
so we need a little filtering, ergo the majority of code in the function.
Edit: it the readRenviron-to-envvar is the best way for you, it would not be difficult to redirect the output of this make call to another file, parse out the relevant lines, and then do readRenviron on that new file. It seems more indirect due to the use of two temp files, but they're cleaned up so that should be nothing to worry about.
I created this random time series:
MM=1584
Z0<-rnorm(MM,8,1.0)#;ts.plot(Z0)
s_1=1.50; p_1=121; p_2=240
s_2=1.25; p_3=361; p_4=480
s_3=1.10; p_5=601; p_6=720
s_4=1.50; p_7=960; p_8=1020
s_5=1.25; p_9=1140; p_10=1320
s_6=1.50; p_11=1369; p_12=1440
a=(Z0[1:p_1-1])
b=(s_1+Z0[p_1:p_2])
c=(Z0[(p_2+1):(p_3-1)])
d=(s_2+Z0[p_3:p_4])
e=(Z0[(p_4+1):(p_5-1)])
f=(s_2+Z0[p_5:p_6])
g=(Z0[(p_6+1):(p_7-1)])
h=(s_3+Z0[p_7:p_8])
i=(Z0[(p_8+1):(p_9-1)])
l=(s_4+Z0[p_9:p_10])
m=(Z0[(p_10+1):(p_11-1)])
n=(s_5+Z0[p_11:p_12])
o=Z0[(p_12+1):MM]
Z=c(a,b,c,d,e,f,g,h,i,l,m,n,o);ts.plot(Z)
abline(v=p_1,col="red");abline(v=p_2,col="red");abline(v=p_3,col="red")
abline(v=p_4,col="red");abline(v=p_5,col="red");abline(v=p_6,col="red")
abline(v=p_7,col="red");abline(v=p_8,col="red");abline(v=p_9,col="red")
abline(v=p_10,col="red");abline(v=p_11,col="red");abline(v=p_12,col="red")
Zm=as.data.frame(Z)
write.csv2(Zm, file="C:/Users/Luca/Dekstop/Zm/Zm1.csv")
I would like to repeat these commands to create 100 series and to save these with write.cs2(...Zm"...".csv).
I don't want to change the file names and repeat the commands all manually.
I searched something useful in other questions but I didn't find it.
The loop has to change only the name of data frame (Zm) and the file names, for each loop.
I'm looking to repeat 100 times the creation of Z0 (Z01, Z02, Z03 ... Z0100) , then Z (Z1, Z2, ... Z100) so Zm (Zm1, Zm2, Zm3... Zm100) and save them in the folder with new file names (folder/Zm1, Zm2, Zm3 etc...) all in 1 command with a loop.
I'm not sure why you want to change the name of the data frames, but dynamically changing the name of the file is straightforward.
for (i in 1:100) { ... write.csv2(Zm, file=paste("C:/Users/Luca/Dekstop/Zm/Zm", i, ".csv", sep = "")) }
If you want to keep the created data frames, why not just simply use a list?
I need to import a list of 36 csv files, but after running the code I get only 26 of them. Probably, 10 files have format problems. Is there a way in R to detect the 10 files that cannot be imported?
If you the file names in a list, you can use the following code:
all <- c("16048.txt", "16062.txt", "16066.txt", "16093.txt", "16095.txt", "16122.txt", "16241.txt", "16360.txt", "16380.txt", "16389.txt", "16510.txt", "16511.txt", "16701.txt", "16729.txt", "16735.txt", "16737.txt", "16761.txt", "16816.txt", "16867.txt", "16876.txt", "16880.txt", "16883.txt", "16884.txt", "16885.txt", "16893.txt", "16904.txt", "16906.txt", "16908.txt", "16929.txt", "16931.txt", "16938.txt", "16943.txt", "16959.txt", "16967.txt", "16968.txt", "16969.txt")
imp <- c("16761.txt", "16959.txt", "16884.txt", "16093.txt", "16883.txt", "16122.txt", "16906.txt", "16737.txt", "16968.txt", "16095.txt", "16062.txt", "16816.txt", "16360.txt", "16893.txt", "16885.txt", "16938.txt", "16048.txt", "16931.txt", "16876.txt", "16511.txt", "16969.txt", "16241.txt", "16967.txt", "16701.txt", "16380.txt", "16510.txt")
Where all is the list of filenames you need and imp is the imperfect result you got. You can get a list of the missing files with:
missing <- all[!all %in% imp]