Rename part of file name based on exact match in contents of another file

Question

I would like to rename a bunch of files by changing only one part of the file name and doing that based on an exact match in a list in another file. For example, if I have

Answer 1

You can perfectly combine your for and while loops to only use mv:

while read from to ; do
  for i in test* ; do
    if [ "$i" != "${i/$from/$to}" ] ; then
      mv $i ${i/$from/$to}
    fi
  done
done < replacements.txt

---

An alternative solution with sed could consist in using the e command that executes the result of a substitution (Use with caution! Try without the ending e first to print what commands would be executed).

Hence:

sed 's/\(\w\+\)\s\+\(\w\+\)/mv sample_\1\.txt sample_\2\.txt/e' replacements.txt

would parse your replacements.txt file and rename all your .txt files as desired.

We just have to add a loop to deal with the other extentions:

for j in .txt .bak .tsv .fq .fq.abc ; do
  sed "s/\(\w\+\)\s\+\(\w\+\)/mv 'sample_\1$j' 'sample_\2$j'/e" replacements.txt
done

(Note that you should get error messages when it tries to rename non-existing files, for example when it tries to execute mv sample_ACGT.fq sample_name1.fq but file sample_ACGT.fq does not exist)

Answer 2

You could use awk to generate commands:

% awk '{print "for files in sample_*; do mv $files ${files/" $1 "/" $2 "}; done" }' replacements.txt 
for files in sample_*; do mv $files ${files/ACGT/name1}; done
for files in sample_*; do mv $files ${files/TTTTTC/longername12}; done
for files in sample_*; do mv $files ${files/ACCCGGG/nam7}; done
for files in sample_*; do mv $files ${files/ACGTA/another4}; done

Then either copy/paste or pipe the output directly to your shell:

% awk '{print "for files in sample_*; do mv $files ${files/" $1 "/" $2 "}; done" }' replacements.txt | bash

If you want the longer match string to be used first, sort the replacements first:

% sort -r replacements.txt | awk '{print "for files in sample_*; do mv $files ${files/" $1 "/" $2 "}; done" }' | bash