Last updated: 2020-06-07

Checks: 7 0

Knit directory: bioinformatics_tips/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200503)

The command set.seed(20200503) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

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Repository version: cbfdeb7

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version cbfdeb7. 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: 


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/security.Rmd

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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 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

Each script you write should serve a certain purpose; for example, you might need a script to convert one file format to another and you can’t find one that’s available online. Since you will invest your time into developing this script, you should ensure that it can be easily reused in the future. You or your colleague may have another file that needs to be converted or you need the conversion to be slightly modified (BED3 instead of BED6).

One simple way of achieving this flexibility is to write a script that is more generalised and one that accepts command line arguments. Using the format converter example, our script may accept two arguments and using these arguments we can easily reuse our script on a different file or output a slightly different output.

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

I have example scripts with code for accepting and processing command line arguments. Each script will also output its usage if no arguments are supplied.

Using Bash.

#!/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.

#!/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.

#!/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 10.15.5

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     

loaded via a namespace (and not attached):
 [1] workflowr_1.6.2 Rcpp_1.0.4.6    rprojroot_1.3-2 digest_0.6.25  
 [5] later_1.0.0     R6_2.4.1        backports_1.1.7 git2r_0.27.1   
 [9] magrittr_1.5    evaluate_0.14   stringi_1.4.6   rlang_0.4.6    
[13] fs_1.4.1        promises_1.1.0  whisker_0.4     rmarkdown_2.1  
[17] tools_4.0.0     stringr_1.4.0   glue_1.4.1      httpuv_1.5.3.1 
[21] xfun_0.14       yaml_2.2.1      compiler_4.0.0  htmltools_0.4.0
[25] knitr_1.28