argparse is a command line argument parser inspired by Python’s “argparse” library. Use this with Rscript to write “#!”-shebang scripts that accept short and long flags/options and positional arguments, generate a usage statement, and set default values for options that are not specified on the command line.
In our working directory we have two example R scripts, named “example.R” and “display_file.R” illustrating the use of the argparse package.
bash$ ls
display_file.R
example.RIn order for a *nix system to recognize a “#!”-shebang line you need
to mark the file executable with the chmod command, it also
helps to add the directory containing your Rscripts to your path:
bash$ chmod ug+x display_file.R example.R
bash$ display_file.R example.R
Here is what “example.R” contains:
bash$ display_file.R example.R
Setting r-universe rmarkdown theme...
#!/usr/bin/env Rscript
# Copyright 2012-2013 Trevor L Davis <[email protected]>
# Copyright 2008 Allen Day
#
# This file is free software: you may copy, redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 2 of the License, or (at your
# option) any later version.
#
# This file is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
suppressPackageStartupMessages(library("argparse"))
# create parser object
parser <- ArgumentParser()
# specify our desired options
# by default ArgumentParser will add an help option
parser$add_argument("-v", "--verbose", action="store_true", default=TRUE,
help="Print extra output [default]")
parser$add_argument("-q", "--quietly", action="store_false",
dest="verbose", help="Print little output")
parser$add_argument("-c", "--count", type="integer", default=5,
help="Number of random normals to generate [default %(default)s]",
metavar="number")
parser$add_argument("--generator", default="rnorm",
help = "Function to generate random deviates [default \"%(default)s\"]")
parser$add_argument("--mean", default=0, type="double",
help="Mean if generator == \"rnorm\" [default %(default)s]")
parser$add_argument("--sd", default=1, type="double",
metavar="standard deviation",
help="Standard deviation if generator == \"rnorm\" [default %(default)s]")
# get command line options, if help option encountered print help and exit,
# otherwise if options not found on command line then set defaults,
args <- parser$parse_args()
# print some progress messages to stderr if "quietly" wasn't requested
if ( args$verbose ) {
write("writing some verbose output to standard error...\n", stderr())
}
# do some operations based on user input
if( args$generator == "rnorm") {
cat(paste(rnorm(args$count, mean=args$mean, sd=args$sd), collapse="\n"))
} else {
cat(paste(do.call(args$generator, list(args$count)), collapse="\n"))
}
cat("\n")By default argparse will generate a help message if it
encounters --help or -h on the command line.
Note how %(default)s in the example program was replaced by
the actual default values in the help statement that
argparse generated.
bash$ example.R –help
Setting r-universe rmarkdown theme...
usage: example.R [-h] [-v] [-q] [-c number] [--generator GENERATOR]
[--mean MEAN] [--sd standard deviation]
options:
-h, --help show this help message and exit
-v, --verbose Print extra output [default]
-q, --quietly Print little output
-c number, --count number
Number of random normals to generate [default 5]
--generator GENERATOR
Function to generate random deviates [default "rnorm"]
--mean MEAN Mean if generator == "rnorm" [default 0]
--sd standard deviation
Standard deviation if generator == "rnorm" [default 1]If you specify default values when creating your
ArgumentParser then argparse will use them as
expected.
bash$ example.R
Setting r-universe rmarkdown theme...
writing some verbose output to standard error...
-1.26552152517213
0.179159755575581
0.403589848296984
0.400180260373932
-0.278200568917447Or you can specify your own values.
bash$ example.R –mean=10 –sd=10 –count=3
Setting r-universe rmarkdown theme...
writing some verbose output to standard error...
9.56069966655805
6.34295818269605
-9.33808681882496If you remember from the example program that --quiet
had action="store_false" and dest="verbose".
This means that --quiet is a switch that turns the
verbose option from its default value of TRUE
to FALSE. Note how the verbose and
quiet options store their value in the exact same
variable.
bash$ example.R –quiet -c 4 –generator=“runif”
Setting r-universe rmarkdown theme...
0.529817214235663
0.350412957835943
0.673064763890579
0.350800399435684If you specify an illegal flag then will print out a usage message and an error message and quit.
bash$ example.R –silent -m 5
Setting r-universe rmarkdown theme...
usage: example.R [-h] [-v] [-q] [-c number] [--generator GENERATOR]
[--mean MEAN] [--sd standard deviation]
example.R: error: unrecognized arguments: --silent -m 5If you specify the same option multiple times then will use the value of the last option specified.
bash$ example.R -c 100 -c 2 -c 1000 -c 7
Setting r-universe rmarkdown theme...
writing some verbose output to standard error...
-1.00932154296064
0.143904886648792
1.01464308736813
-0.756123757668264
-0.0323723040210964
0.198002636684946
-1.83732206552719argparse can also parse positional arguments. Below we
give an example program display_file.R, which is a program
that prints out the contents of a single file (the required positional
argument, not an optional argument) and which accepts the normal help
option as well as an option to add line numbers to the output.
bash$ display_file.R –help
Setting r-universe rmarkdown theme...
usage: display_file.R [-h] [-n] file
positional arguments:
file File to be displayed
options:
-h, --help show this help message and exit
-n, --add_numbers Print line number at the beginning of each line [default]bash$ display_file.R –add_numbers display_file.R
Setting r-universe rmarkdown theme...
1 #!/usr/bin/env Rscript
2 # Copyright 2012-2013 Trevor L Davis <[email protected]>
3 #
4 # This file is free software: you may copy, redistribute and/or modify it
5 # under the terms of the GNU General Public License as published by the
6 # Free Software Foundation, either version 2 of the License, or (at your
7 # option) any later version.
8 #
9 # This file is distributed in the hope that it will be useful, but
10 # WITHOUT ANY WARRANTY; without even the implied warranty of
11 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 # General Public License for more details.
13 #
14 # You should have received a copy of the GNU General Public License
15 # along with this program. If not, see <http://www.gnu.org/licenses/>.
16 suppressPackageStartupMessages(library("argparse"))
17
18 parser <- ArgumentParser()
19 parser$add_argument("-n", "--add_numbers", action="store_true", default=FALSE,
20 help="Print line number at the beginning of each line [default]")
21 parser$add_argument("file", nargs=1, help="File to be displayed")
22
23 args <- parser$parse_args()
24
25 file <- args$file
26
27 if( file.access(file) == -1) {
28 stop(sprintf("Specified file ( %s ) does not exist", file))
29 } else {
30 file_text <- readLines(file)
31 }
32
33 if(args$add_numbers) {
34 cat(paste(1:length(file_text), file_text), sep = "\n")
35 } else {
36 cat(file_text, sep = "\n")
37 }bash$ display_file.R non_existent_file.txt
Setting r-universe rmarkdown theme...
Error: Specified file ( non_existent_file.txt ) does not exist
Execution haltedbash$ display_file.R
Setting r-universe rmarkdown theme...
usage: display_file.R [-h] [-n] file
display_file.R: error: the following arguments are required: file