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

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 these file names:
sample_ACGTA.txt
sample_ACGTA.fq.abc
sample_ACGT.txt
sample_TTTTTC.tsv
sample_ACCCGGG.fq
sample_ACCCGGG.txt
otherfile.txt
and I want to find and replace based on these exact matches, which are found in another file called replacements.txt:
ACGT name1
TTTTTC longername12
ACCCGGG nam7
ACGTA another4
So that the desired resulting file names would be
sample_another4.txt
sample_another4.fq.abc
sample_name1.txt
sample_longername12.tsv
sample_nam7.fq
sample_nam7.txt
otherfile.txt
I do not want to change the contents. So far I have tried sed and mv based on my search results on this website. With sed I found out how to replace the contents of the file using my list:
while read from to; do
sed -i "s/$from/$to/" infile ;
done < replacements.txt,
and with mv I have found a way to rename files if there is one simple replacement:
for files in sample_*; do
mv "$files" "${files/ACGTA/another4}"
done
But how can I put them together to do what I would like?
Thank you for your help!

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