Last updated: 2020-05-09

Checks: 7 0

Knit directory: bioinformatics_tips/

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The results in this page were generated with repository version 05424eb. 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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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/get_option.Rmd) and HTML (docs/get_option.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 169cfdf davetang 2020-05-09 Build site.
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