Last updated: 2023-01-23

Checks: 7 0

Knit directory: bioinformatics_tips/

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Repository version: f3de727

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The results in this page were generated with repository version f3de727. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


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File Version Author Date Message
Rmd f3de727 Dave Tang 2023-01-23 GNU getopt
html 772b06a Dave Tang 2022-09-05 Build site.
Rmd 1a2198d Dave Tang 2022-09-05 Pos and opt args with R
html 2106d5e Dave Tang 2022-08-15 Build site.
Rmd 2df43f5 Dave Tang 2022-08-15 Include Python example
html e9934e7 davetang 2020-06-07 Security basics
html 56b7e19 davetang 2020-05-10 Build site.
Rmd 778bf20 davetang 2020-05-10 Copy code button
html 04be0ae davetang 2020-05-09 Build site.
Rmd f8b797f davetang 2020-05-09 No TOC
html 60d127f davetang 2020-05-09 Build site.
html 169cfdf davetang 2020-05-09 Build site.
Rmd 83ae7f7 davetang 2020-05-09 Command line arguments

If you have used Unix tools on the command line, you may have noticed that you can provide different arguments/options to the tool to modify its behaviour. For example using the ls command by itself will simply return files and directories (without a . prefix) that exist in your current working directory.

ls
analysis
bioinformatics_tips.Rproj
code
data
docs
LICENSE
output
README.md
ref
script
_workflowr.yml

If you want to show all files, use the -a (short) or --all (long) option.

ls -a
.
..
analysis
bioinformatics_tips.Rproj
code
data
docs
.git
.gitattributes
.gitignore
LICENSE
output
README.md
ref
.Rhistory
.Rprofile
.Rproj.user
script
_workflowr.yml

You can write scripts in different languages that mimic this behaviour. It is preferable to write scripts that accept command line arguments because it makes it easy to reuse the script on a different dataset or rerun the script using different parameters. In addition, this makes it easy to incorporate the script into a bioinformatics pipeline.

Some concepts to understand are usage, short and long options, and positional and optional arguments.

  • The usage explains the details of your script and it is good practice to display a script’s usage when no arguments are provided.
  • Short and long options are simply a preference but I prefer long options as they are readable and informative. Most modern day command line tools provide both options.
  • Positional arguments are mandatory arguments that need to be specified in a specific order. For example the cp command will copy the first positional argument to the last positional argument. Optional arguments are non-mandatory and can be specified using short and long options; their order does not matter.

Below are examples of writing scripts that accept command line arguments in Python, Bash, R, and Perl.

Python

In Python use the argparse module.

#!/usr/bin/env python3
#
# based on the argparse tutorial https://docs.python.org/3/howto/argparse.html
#

import argparse
parser = argparse.ArgumentParser()

#
# positional arguments
#

# default type is string
parser.add_argument(
        "echo",
        help = "display a string",
)
# specify integer type
parser.add_argument(
        "number",
        help = "display a number",
        type = int
)

#
# optional arguments
#

# short and long options
# store True if specified
parser.add_argument(
        "-v",
        "--verbose",
        help = "verbose mode",
        action = "store_true"
)

# set choices for argument and default value
parser.add_argument(
        "-p",
        "--threads",
        help = "number of threads",
        choices = range(1,9),
        default = 2,
        type = int
)

args = parser.parse_args()

if args.verbose:
    print("Verbose mode")

if args.threads:
    print("Using %d threads" % args.threads)

print("%s's type is %s" % (args.echo, type(args.echo)))
print("%s's type is %s" % (args.number, type(args.number)))

If you run the Python script by itself, a simple usage will be displayed. (Ignore the || true command, which is only needed because this document is generated programmatically.)

code/python/parse_arg.py || true
usage: parse_arg.py [-h] [-v] [-p {1,2,3,4,5,6,7,8}] echo number
parse_arg.py: error: the following arguments are required: echo, number

You can get a more detailed usage by using the help argument.

code/python/parse_arg.py -h
usage: parse_arg.py [-h] [-v] [-p {1,2,3,4,5,6,7,8}] echo number

positional arguments:
  echo                  display a string
  number                display a number

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         verbose mode
  -p {1,2,3,4,5,6,7,8}, --threads {1,2,3,4,5,6,7,8}
                        number of threads

Run the script with positional and optional arguments.

code/python/parse_arg.py foobar 1984 -v
Verbose mode
Using 2 threads
foobar's type is <class 'str'>
1984's type is <class 'int'>

Bash

In Bash you can use the getopts command.

#!/usr/bin/env bash

usage() {
  # redirect STDOUT to STDERR
  echo "Usage: $0 [ -f FILE ] [ -t INT ]" 1>&2 
  exit 1
}

while getopts ":f:t:" options; do
  case "${options}" in
    f)
      file=${OPTARG}
      ;;
    t)
      thread=${OPTARG}
      regex='^[1-9][0-9]*$'
      if [[ ! $thread =~ $regex ]]; then
        usage
      fi
      ;;
    :)
      echo "Error: -${OPTARG} requires an argument."
      exit 1
      ;;
    *)
      usage ;;
  esac
done

# OPTIND is the number of arguments that are options or arguments to options
if [ $OPTIND -ne 5 ]; then
  usage
fi

printf "File: %s\nThreads: %d\n" $file $thread

exit 0

Usage.

code/unix/get_option.sh || true
Usage: code/unix/get_option.sh [ -f FILE ] [ -t INT ]

However, the GNU getopt tool allows you to mix short and long options with positional arguments too.

cat code/unix/getopt.sh
#!/usr/bin/env bash
#
# Adapted from https://www.shellscript.sh/examples/getopt/
#
set -euo pipefail

alpha=unset
beta=unset
gamma=unset
delta=unset

usage(){
>&2 cat << EOF
Usage: $0
   [ -a | --alpha ]
   [ -b | --beta ]
   [ -g | --gamma input ] 
   [ -d | --delta input ]
   <infile> [infiles]
EOF
exit 1
}

args=$(getopt -a -o abhc:d: --long alpha,beta,help,gamma:,delta: -- "$@")
if [[ $? -gt 0 ]]; then
  usage
fi

eval set -- ${args}
while :
do
  case $1 in
    -a | --alpha)   alpha=1    ; shift   ;;
    -b | --beta)    beta=1     ; shift   ;;
    -h | --help)    usage      ; shift   ;;
    -c | --gamma)   gamma=$2   ; shift 2 ;;
    -d | --delta)   delta=$2   ; shift 2 ;;
    # -- means the end of the arguments; drop this, and break out of the while loop
    --) shift; break ;;
    *) >&2 echo Unsupported option: $1
       usage ;;
  esac
done

if [[ $# -eq 0 ]]; then
  usage
fi

>&2 echo "alpha   : ${alpha}"
>&2 echo "beta    : ${beta} "
>&2 echo "gamma   : ${gamma}"
>&2 echo "delta   : ${delta}"
>&2 echo "Parameters remaining are: $@"
exit 0

Usage.

code/unix/getopt.sh || true
Usage: code/unix/getopt.sh
   [ -a | --alpha ]
   [ -b | --beta ]
   [ -g | --gamma input ] 
   [ -d | --delta input ]
   <infile> [infiles]

R

In R use the optparse library.

#!/usr/bin/env Rscript
#
# Example script using both positional and optional arguments. For more
# examples, see:
#
#     https://cran.r-project.org/web/packages/optparse/vignettes/optparse.html
#

suppressPackageStartupMessages(library(optparse))

# optional args
option_list <- list(
   make_option(c("-p", "--threads"), type = "integer", default = 2, help =
               "Number of threads to use (default = %default)"),
   make_option(c("-v", "--verbose"), action = "store_true", default = FALSE,
               help = "Verbose mode (default = %default)")
)

# create your own usage
opt_parse <- OptionParser(usage = "%prog [options] infile <infile2> ...",
                          option_list = option_list)

# set positional_arguments to TRUE
opt <- parse_args(opt_parse, positional_arguments = TRUE)

# print usage if no positional args provided
if (length(opt$args) == 0){
   print_help(opt_parse)
   stop("Please provide an input file")
}

if (opt$options$verbose){
   message("Verbose mode activated")
}
message(paste0("Using ", opt$options$threads, " threads"))

for (file in opt$args){
   if(!file.exists(file)){
      stop(paste0(file, " does not exist"))
   }
   message(paste0("Processing ", file))
}

message("Done")
quit()

Usage.

code/r/optparse.R || true
Loading .Rprofile for the current workflowr project
This is workflowr version 1.7.0
Run ?workflowr for help getting started
Current settings:
  user.email: davetingpongtang@gmail.com
  user.name: Dave Tang
The settings above will be overwritten.
Current Git user.name:  Dave Tang
Current Git user.email: davetingpongtang@gmail.com
Other Git settings:

Usage: code/r/optparse.R [options]


Options:
    -f READ1.FASTQ1, --first=READ1.FASTQ1
        first read pair

    -s READ2.FASTQ, --second=READ2.FASTQ
        second read pair

    -t THREAD, --thread=THREAD
        number of threads to use

    -h, --help
        Show this help message and exit

Perl

In Perl use the Getopt::Long package (or Getopt::Std).

#!/usr/bin/env perl

use warnings;
use strict;
use Getopt::Long;

my $fastq1  = "";
my $fastq2  = "";
my $thread  = 8;
my $verbose = 0;
my $help    = 0;

GetOptions ("thread=i" => \$thread,   # numeric
            "first=s"  => \$fastq1,   # string
            "second=s" => \$fastq2,   # string
            "verbose"  => \$verbose,  # flag
            "help"     => \$help)     # flag
|| die("Error in command line arguments\n");

if ($fastq1 eq "" || $fastq2 eq "" || $help == 1){
   usage()
}

if ($verbose){
   print join("\n", "First: $fastq1", "Second: $fastq2", "Thread: $thread"), "\n";
}

sub usage {
print STDERR <<EOF;
Usage: $0 -f read1.fastq -s read2.fastq -t 8

Where:   -f, --first  FILE     first read pair
         -s, --second FILE     second read pair
         -t, --thread INT      number of threads to use (default 8)
         -v, --verbose         print out arguments
         -h, --help            this helpful usage message

EOF
exit();
}

__END__

Usage.

code/perl/getopts.pl
Usage: code/perl/getopts.pl -f read1.fastq -s read2.fastq -t 8

Where:   -f, --first  FILE     first read pair
         -s, --second FILE     second read pair
         -t, --thread INT      number of threads to use (default 8)
         -v, --verbose         print out arguments
         -h, --help            this helpful usage message

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     bslib_0.4.1      compiler_4.2.0   pillar_1.7.0    
 [5] later_1.3.0      git2r_0.30.1     jquerylib_0.1.4  tools_4.2.0     
 [9] getPass_0.2-2    digest_0.6.30    jsonlite_1.8.3   evaluate_0.17   
[13] tibble_3.1.7     lifecycle_1.0.3  pkgconfig_2.0.3  rlang_1.0.6     
[17] cli_3.4.1        rstudioapi_0.13  yaml_2.3.6       xfun_0.34       
[21] fastmap_1.1.0    httr_1.4.3       stringr_1.4.0    knitr_1.39      
[25] sass_0.4.1       fs_1.5.2         vctrs_0.5.0      rprojroot_2.0.3 
[29] glue_1.6.2       R6_2.5.1         processx_3.8.0   fansi_1.0.3     
[33] rmarkdown_2.17   callr_3.7.3      magrittr_2.0.3   whisker_0.4     
[37] ps_1.7.2         promises_1.2.0.1 htmltools_0.5.2  ellipsis_0.3.2  
[41] httpuv_1.6.6     utf8_1.2.2       stringi_1.7.6    cachem_1.0.6    
[45] crayon_1.5.2