How to rename a heap of files with one tidy script

Suppose you have a lot of files and you want to change something in each file name. If you want the same change done to all of them, it is realtively easy, for example, change file extention from .txt to .tab:

for file in *.txt
do
  mv "$file"" "${file/.txt/.tab}"
done

where “for” starts the loop, "*.txt" specifies all files in the directory that have names like mike.txt, log.txt, etc, “mv” changes an old name for a new name, “do” and “done” mark the repeated action

Now, how to remove all the pesky white spaces, essentially the same thing:

IFS="\n"
for file in *.txt;
do
    mv "$file" "${file//[[:space:]]}"
done

Now, if your situation is a little be more complicated, namely, you have tons of files and an index file, that corresponds part of the name you want to change with a thing you want to change it for (say, swipe a barcode sequence in the file name for aa sample name it belongs to), you can use this neat little script, that I found in the depth of stackoverflow, credits belong to @eduard-i

#!/bin/bash
while IFS='' read -r line || [[ -n "$line" ]]; do
        NR=$(echo "$line" | cut -f 2)
        NAME=$(echo "$line" | cut -f 1)
        if [ -f "FlowcellNum_R1_${NR}.fastq" ] ; then
                mv "FlowcellNum_R1_${NR}.fastq" "FlowcellNum_R1_${NAME}.fastq"
        fi
done < indexfile

where

while IFS='' read -r line || [[ -n "$line" ]];

reads the index file,

NR=$(echo "$line" | cut -f 2)

reads the barcode (the part of the file name I want to change is in the second column of my index correspondence file)

NAME=$(echo "$line" | cut -f 1)

reads the corresponding sample name, which is in my first column of index correspondence file

if [ -f "FlowcellNum_R1_${NR}.fastq" ] ; then

checks if the file name fits the pattern of names I want to change, and

mv "FlowcellNum_R1_${NR}.fastq" "FlowcellNum_R1_${NAME}.fastq"

renames the file.

my barcode correspondence (indexfile) looks like this:

Sample01 ACAAGCTA Sample02 AAACATCG …

and files are renamed from FlowcellNum_R1_ACAAGCTA.fastq to FlowcellNum_R1_Sample1.fastq respectively