rename fastq.gz file name

Question

I have hundreds fast.gz files, and they have the same format of file name:

5809029_GWU_DNA_269_L001_R1_001.fastq.gz
5809030_GWU_DNA_269_L001_R1_001.fastq.gz

How do I change the first and the second underscores to dots? eg:

5809029.GWU.DNA_269_L001_R1_001.fastq.gz
5809030.GWU.DNA_269_L001_R1_001.fastq.gz

without changing the remaining underscores?

I have tried rename 's/_GWU_DNA/\.GWU\.DNA/' *gz, it didn't change anything. So I'm thinking about a for loop, any idea? Thank you!

Welcome! I'm trying your command with no issues, it renames the files. You don't need to escape the dots in the substitution. — schrodingerscatcuriosity, Dec 03 '19 at 16:32
I'm not familiar with MAC, I don't know if `rename` is part of the system, or if it is, how it behaves, so I don't know if you have to install something, sorry. — schrodingerscatcuriosity, Dec 03 '19 at 16:59
I'm on Linux Mint, bash version `GNU bash, versión 4.4.19(1)` — schrodingerscatcuriosity, Dec 03 '19 at 17:03
macOS does not have a `rename` utility by default, so if you have one, it must have been installed separately. There are [different variations of this command though](https://unix.stackexchange.com/questions/229230/whats-with-all-the-renames-prename-rename-file-rename). — Kusalananda, Dec 03 '19 at 17:24

score 1 · Answer 1 · edited Dec 03 '19 at 18:29

1

Here you have a mv possibility:

for f in *_GWU_*.gz; do 
  mv "$f" "${f/_GWU_/.GWU.}"
done

edited Dec 03 '19 at 18:29

Kusalananda

answered Dec 03 '19 at 18:26

1 Answers1