When I analyze data, I like to write a series of short scripts rather than one long piece of code. I find that by keeping each step of the analysis in its own file, I can better grasp what I’m doing.

The result will be a series of numbered scripts that might look something like this:

1_get_data.R
2_clean_data.R
3_combine_data.R
4_analyze_data.R

As the analysis grows, I accumulate more scripts. And often, I realize that I need to insert a new script somewhere in the middle of the pipeline, meaning the rest of the scripts need to be renumbered. Also, when I accumulate more than 10 scripts, suddenly my computer thinks that 10_ comes before 1_. So I need to pad all the files with leading zeroes.

Of course this renumbering is a simple task. But it’s also a pain in the butt. And so I wrote a bash script that will do it for me.

Here’s an example. Suppose I delete the first file in my pipeline:

2_clean_data.R
3_combine_data.R
4_analyze_data.R

To renumber the remaining files, I execute my script, which is called pad_file. It will renumber the remain files like this:

 2_clean_data.R  ---->  01_clean_data.R
 3_combine_data.R  ---->  02_combine_data.R
 4_analyze_data.R  ---->  03_analyze_data.R

Then I realize that I need to move the first file to the end of the pipeline. I’m not sure what it’s number should be, so I just give it something high, say 05. I rename it with the mv command as:

mv 01_clean_data.R  05_clean_data.R

Then I renumber everything with pad_file:

 02_combine_data.R  ---->  01_combine_data.R
 03_analyze_data.R  ---->  02_analyze_data.R
 05_clean_data.R  ---->  03_clean_data.R

When there are only a handful of numbered files, this renumbering command doesn’t save much time. But when there are 20 scripts, it’s a life saver.

Here’s the code for the renumbering script. Execute it in the directory containing the files you want renumbered. It will first show you what it’s going to rename, and then prompt you to proceed.

If you want the script to be executable from anywhere, put it in your PATH and give it a name you like. You can then execute it by typing that name in the terminal. I call mine pad_file.

#!/bin/bash

# A bash script to renumber files

# test rename
#-------------------------------------------

# get files containing number
files=$( ls | grep '^[0-9]' | sort --version-sort )

# output color
RED='\033[0;31m'


n=1;
for f in $files; do
    
    # strip numbers from file
    file_name=$( printf '%s\n' "${f//[[:digit:]]/}" )

    # pad file number
    file_number=$( printf %02d $n)

    # new file name
    file_new="$file_number""$file_name"

    echo $(tput setaf 2) $f  $(tput setaf 5) '---->' $(tput setaf 4) $file_new $(tput setaf 7)

    let n="$n+1"

done



# actually rename
#-------------------------------------------

echo Type GO to rename files
read test 

if [ $test == "GO" ] ; 
then

    echo renaming ...

    n=1;
    for f in $files; do
	
	# strip numbers from file
	file_name=$( printf '%s\n' "${f//[[:digit:]]/}" )

	# pad file number
	file_number=$( printf %02d $n)

	# new file name
	file_new="$file_number""$file_name"
	
	# test if file names are different
	# rename files
	mv $f $file_new

	let n="$n+1"

    done

fi