Changing part of the name of many files to unique names, using a spreadsheet of names

Question

I need some help. I want to rename very many files with unique filenames using bash. I want to keep part of the original filename.

For example:

current file name	new file name
F1.R23.fastq.gz	10_1.F1.R23.fastq.gz
F2.R7.fastq.gz	empty_3_1.F2.R7.fastq.gz
F32.R3.fastq.gz	63_3.F32.R3.fastq.gz
F5.R7.fastq.gz	Blank_3.F5.R7.fastq.gz
F2.R2.fastq.gz	N5_1.F2.R2.fastq.gz

What I have, is a file containing a column with the original names, and a column containing what I want to add to the names. Like so:

file	sample
F1.R23.fastq.gz	10_1
F2.R7.fastq.gz	empty_3_1
F32.R3.fastq.gz	63_3
F5.R7.fastq.gz	Blank_3
F2.R2.fastq.gz	N5_1

I would really appreciate if anybody has a way of doing this. I have potentially thousands of files to rename, some with complicated names and in a random order, and so it’s not really feasible to do this by hand.

Thank you!

Answer 1

First, create a csv file called files-to-rename.csv, or convert the spreadsheet you have to CSV format. The contents of the file should be like this:

F1.R23.fastq.gz,10_1
F2.R7.fastq.gz,empty_3_1
F32.R3.fastq.gz,63_3
F5.R7.fastq.gz,Blank_3
F2.R2.fastq.gz,N5_1

Then run this command, making sure you are in the same directory as the files:

while IFS=$',\r' read -r source dest ; do
  mv -v "$source" "${dest}.${source}"
done < files-to-rename.csv

The above will not work if the csv file has DOS line endings. You can use the dos2unix files-to-rename.csv command to make sure the file is in UNIX line endings.

---

Otherwise, use this safer snippet below:

while read line; do
  source=$(echo $line | cut -d, -f1)
  dest=$(echo $line | cut -d, -f2)

  mv -v "$source" "${dest}.${source}"
done < files-to-rename.csv