manipulate string from command line argument-CodePudding

I'm calling in an argument with optparse, but I'm needing the string of the resulting argument (variable x) to be in the format "test", "test2", "test3" (quotations separated by commas):

# Set up command line arguments 

library("optparse")

option_list = list(
  make_option(c("--test"), type="character", default=NULL, 
              help="test", metavar="character")

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

# grab argument into x variable

x <- (opt$pathcsv)
print(x)

Entering the command line :

Rscript --vanilla riboeclip_ma.R --pathcsv="test test2 test3"

output is a character type:

"test test2 test3"

However, I would like the format of the x variable to be "test", "test2", "test3"

My code is setup like this (notice how I have "test", "test2", "test3" in a vector):

all_counts.poly.colData <-
   data.frame(Condition =
                c("test", "test2", "test3"))

However, I'd like to pass that x variable instead to achieve the same result (I'm trying to automate this process).

all_counts.poly.colData <-
   data.frame(Condition =
                c(x))

Please let me know if there is a better way to do this, as I'm still new to R and started playing around with the command line arguments yesterday.

CodePudding user response：

Use splitstr from base R to split it into a vector:

strsplit(opt$pathcsv, " ")[[1]]

If you want to add in commas you can use gsub:

gsub(" ", ", ", opt$pathcsv)
[1] "test, test2, test3"

If you want literal quotes use dQuote applied to each and then paste it back together:

paste(sapply(strsplit(opt$pathcsv, " ")[[1]], dQuote), collapse = ",")
[1] "“test”,“test2”,“test3”"

Based on your question you should use strsplit to replicate what you've hardcoded:

data.frame(Condition =
                c("test1", "test2", "test3"))
  Condition
1      test
2     test2
3     test3

x <- strsplit(opt$pathcsv, " ")[[1]]

data.frame(Condition = x)
 Condition
1      test
2     test2
3     test3

c("test", "test1", "test2") is a character vector and you should not try to replicate the syntax of creating a character vector by trying to add in quotes and commas. Instead, parse your command line argument directly into a character vector:

all(strsplit(opt$pathcsv, " ")[[1]] == c("test", "test2", "test3"))
[1] TRUE