Handling Command Line Arguments in R with Optparse and String Manipulation

Introduction

When working with command line arguments in R, it’s often necessary to manipulate the input values to suit your specific needs. In this article, we’ll explore how to handle command line arguments using the optparse package in R, and then use string manipulation techniques to modify the output.

Setting Up Command Line Arguments

To begin, let’s set up a basic command line argument using optparse. We’ll create an option_list that defines two options: one for a character value (--test) with a default value of NULL, and another for a path csv file.

library("optparse")

# Create an option list
option_list = list(
  make_option(c("--test"), type="character", default=NULL, 
              help="test", metavar="character"),
  
  make_option(c("--pathcsv"), type="character", default="", 
              help="Path to csv file")
)

We then create an OptionParser object and pass our option_list to it.

# Create an OptionParser object
opt_parser = OptionParser(option_list=option_list);

Finally, we call the parse_args() function on our parser to retrieve the parsed command line arguments.

# Parse the command line arguments
opt = parse_args(opt_parser);

Accessing Command Line Arguments

To access the parsed command line arguments, we can simply use the opt variable. However, in this case, the value of --test is a character string containing multiple values separated by whitespace.

# Get the path csv file from the opt variable
x <- (opt$pathcsv)

The value of x is "test test2 test3", which is a single character string.

Splitting and Unlisting Values

To split the x value into individual strings, we can use the strsplit() function to split on whitespace.

# Split x into individual strings using strsplit()
x1 <- unlist(strsplit(x, '\\s+'))

The resulting x1 vector contains three elements: "test", "test2", and "test3".

Collating Strings with Commas

To collate these individual strings into a single string with commas separating each value, we can use the paste0() function to concatenate the strings, followed by the collapse argument set to a comma.

# Paste the individual strings together using paste0()
x2 <- paste0(sprintf('"%s"', x1), collapse = ',')

The resulting x2 string is "test","test2","test3".

Displaying Strings

To display these collated strings without escaping quotes, we can use the cat() function.

# Display the collated string using cat()
cat(x2)

The output is "test","test2","test3", which is displayed without escaping quotes.

Conclusion

In this article, we explored how to handle command line arguments in R using the optparse package and string manipulation techniques. We created a basic command line argument setup, accessed parsed values, split individual strings, collated them with commas, and displayed them without escaping quotes. These techniques can be used in a variety of scenarios where working with command line arguments is necessary.

Additional Resources

For more information on optparse, see the official R documentation:

library(rdoc)
?optparse

For additional string manipulation techniques in R, see the following articles:

String Manipulation in R

Example Use Cases

Here’s an example use case where we create a simple script to parse command line arguments and manipulate them:

library("optparse")

# Create an option list
option_list = list(
  make_option(c("--test"), type="character", default=NULL, 
              help="test", metavar="character"),
  
  make_option(c("--pathcsv"), type="character", default="", 
              help="Path to csv file")
)

# Create an OptionParser object
opt_parser = OptionParser(option_list=option_list);

# Parse the command line arguments
opt = parse_args(opt_parser);

# Get the path csv file from the opt variable
x <- (opt$pathcsv)

# Split x into individual strings using strsplit()
x1 <- unlist(strsplit(x, '\\s+'))

# Paste the individual strings together using paste0()
x2 <- paste0(sprintf('"%s"', x1), collapse = ',')

You can run this script from the command line by passing in the desired arguments:

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

The output will be displayed without escaping quotes.

Last modified on 2024-03-23