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
#!/usr/bin/env Rscript
# Copyright 2012-2013 Trevor L Davis <trevor.l.davis@gmail.com>
# 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
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
writing some verbose output to standard error...
-0.297358523624249
-1.25237729627517
2.19208471401075
0.568027744879793
-0.238502197273274Or you can specify your own values.
bash$ example.R –mean=10 –sd=10 –count=3
writing some verbose output to standard error...
13.0666007054686
-3.34990224224591
-1.1200086755296If 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”
0.875761628383771
0.152897638967261
0.667401979677379
0.0258402647450566If you specify an illegal flag then will print out a usage message and an error message and quit.
bash$ example.R –silent -m 5
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
writing some verbose output to standard error...
-0.727982002902575
1.4232203929957
0.0386516210512271
-0.933989857153843
-0.512253440710936
-0.89176065255711
1.30489222419739argparse 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
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
1 #!/usr/bin/env Rscript
2 # Copyright 2012-2013 Trevor L Davis <trevor.l.davis@gmail.com>
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
Error: Specified file ( non_existent_file.txt ) does not exist
Execution haltedbash$ display_file.R
usage: display_file.R [-h] [-n] file
display_file.R: error: the following arguments are required: file