Command line arguments

Last updated: 2020-05-09

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Rmd	83ae7f7	davetang	2020-05-09	Command line arguments

Each script you write will serve a certain purpose; for example, a script to convert one file format to another (if such a script doesn’t already exist). Since you will invest your time into writing this script, you should ensure that it can be reused, at the very least, by yourself. You may have another file that you need to convert or you want to convert the file in a slightly different manner (BED3 instead of BED6).

One simple way of achieving this flexibility is to write a script that accepts command line arguments. Using the format converter example, our script may accept two arguments.

psl_to_bed.pl -i input.psl -f bed6 > output.bed

I have example scripts with code for accepting and processing command line arguments.

Using Bash.

cat code/unix/get_option.sh

#!/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

Using R.

cat code/r/optparse.R

#!/usr/bin/env Rscript

library(optparse)

option_list <- list(
   make_option(c("-f", "--first"), type = "character",  help = "first read pair", metavar = "read1.fastq1"),
   make_option(c("-s", "--second"), type = "character", help = "second read pair", metavar = "read2.fastq"),
   make_option(c("-t", "--thread"), type = "integer", help = "number of threads to use", default = 8)
)

opt <- parse_args(OptionParser(option_list=option_list))

if(any(is.null(opt$first), is.null(opt$second))){
   print_help(OptionParser(option_list=option_list))
   quit(status = 1)
}

message(paste0("Read 1: ", opt$first, "\nRead 2: ", opt$second, "\nThread: ", opt$thread))
quit(status = 0)

Using Perl.

cat code/perl/getopts.pl

#!/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__

sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6    rprojroot_1.3-2 digest_0.6.25   later_1.0.0    
 [5] R6_2.4.1        backports_1.1.6 git2r_0.26.1    magrittr_1.5   
 [9] evaluate_0.14   stringi_1.4.6   rlang_0.4.5     fs_1.4.1       
[13] promises_1.1.0  whisker_0.4     rmarkdown_2.1   tools_4.0.0    
[17] stringr_1.4.0   glue_1.4.0      httpuv_1.5.2    xfun_0.13      
[21] yaml_2.2.1      compiler_4.0.0  htmltools_0.4.0 knitr_1.28

Command line arguments

Dave Tang

2020-05-09