This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Batch Renaming Files

Hello BioStar Community,

I would like to rename multiple files in a folder using R script (or scripts written in Python or Perl).

The files in the folder look like:

  1. ABCD123QW.txt
  2. ABCD345XB.txt
  3. ....

And I have a text file which contains Old Names and corresponding New Names:

  1. Old Name New Name
  2. ABCD123QW.txt AL001.txt
  3. ABCD345XB.txt AL002.txt
  4. ... ...

I am a novice in the field of bioinformatics, could anyone help with the file renaming issue?

r python perl snp genome
• 6,018 views • link
written by Tastulek • Tastulek

This is a screenshot after executing the bash script two times.

The 1st time, only one file was renamed, but no error message. The 2nd time, an error message popped up, as shown in the screenshot, which is expectable

• 0 views • link
written by Tastulek • Tastulek

The Screenshot:

  1. MacBook-Pro:BashCode altaic$ ls
  2. ABCD123QW.txt ABCD345XB.txt input.txt script.sh
  3. MacBook-Pro:BashCode altaic$ bash script.sh input.txt
  4. MacBook-Pro:BashCode altaic$ ls
  5. ABCD345XB.txt AL001.txt input.txt script.sh
  6. MacBook-Pro:BashCode altaic$ bash script.sh input.txt
  7. mv: ABCD123QW.txt: No such file or directory
  8. MacBook-Pro:BashCode altaic$
• 0 views • link
written by Tastulek • Tastulek

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

All of your comments regarding bash script should have gone under @Arup's answer.

• 0 views • link
written by GenoMax GenoMax

2 answers

Here's a solution in Python. It will work with different operating systems (Windows, Linux, MacOS, etc.). Make sure the script is in the same directory as the files you want to rename.

Python code (script.py)

import os
import sys

with open(sys.argv[1]) as fh:
    for line in fh:
        sl = line.strip().split(",")
        old_name = sl[0]
        new_name = sl[1]
        os.rename(old_name, new_name)

How to use

python script.py input.txt

Input.txt

ABCD123QW.txt,AL001.txt
ABCD345XB.txt,AL002.txt

Demo

Look at the screenshot of my terminal on Mac. First I display all files that are in the directory (ABCD123QW.txt, ABCD345XB.txt, input.txt, script.py). Then, I run the script and list files again. You can see that two text files were renamed to AL001.txt and AL002.txt.

enter image description here

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Thank you for the Python script! But I am having problems with executing the script...

>>> os.listdir()
['ABCD345XB.txt', 'input.txt', 'ABCD123QW.txt', 'script.py']
>>> python script.py input.txt
SyntaxError: invalid syntax
>>>
• 0 views • link
updated by GenoMax GenoMax • written by Tastulek • Tastulek

Python scripts need to be executed from the command prompt (under Windows) or terminal (under Linux/MacOs). The prompt >>> indicates that you are now in an interactive Python interpeter session, also called the “Python shell”. This is different from the normal terminal command prompt.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Thank you for the note!

I switched to the terminal (Mac), and ran the script, but still there was an error message:

>>> pprint(dirlist)
['ABCD345XB.txt', 'input.txt', 'ABCD123QW.txt', 'script.py']
>>>  python script.py input.txt
  File "<stdin>", line 1
    python script.py input.txt
    ^
IndentationError: unexpected indent
>>>
• 0 views • link
updated by GenoMax GenoMax • written by Tastulek • Tastulek

I updated my answer by adding a screenshot of my terminal on Mac.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Thank you very much, the python code script.py) worked well!

By the way, why does the python code work in Mac terminal [--- -bash --- 80 x 24], but not in python [--- python --- 80 x 24]?

• 0 views • link
written by Tastulek • Tastulek

I have a bash script to do the same thing but it requires comma-separated file as input.

#!/bin/bash
INPUT="$1"
IFS=,
[ ! -f "$INPUT" ] && { echo "$INPUT file not found"; exit 99; }
while read old_name new_name
do
rename "$old_name" "$new_name" # mv or rename
done < "$INPUT"

How to use:

bash script.sh input.txt

Input.txt structure:

Do not include any header.

ABCD123QW.txt,AL001.txt
ABCD345XB.txt,AL002.txt
• 0 views • link
written by Arup Ghosh Arup Ghosh

Arup, Thank you for the bash script!

• 0 views • link
written by Tastulek • Tastulek

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. You can accept multiple answers as correct.
Upvote|Bookmark|Accept

• 0 views • link
written by GenoMax GenoMax

I have executed the bash script, and it worked! But unfortunately, only the name of the first file was changed to AL001, but not the other files...

Any solutions for this?

• 0 views • link
written by Tastulek • Tastulek

Can you share error you are getting or first few lines of the csv file you are using, the script working perfectly fine in my computer with multiple file name as input.

• 0 views • link
written by Arup Ghosh Arup Ghosh

Log in to answer this question.

More posts like this