how to rename or time bunch of file names in fasta file

Question

[venkateshbiotech]

Hi everyone

I have almost more than 1000 MAGS with the following file names.

GCF_029211165.1_ASM2921116v1_genomic.fa

I want them to make it tidy before my analysis, something like this GCF_029211165.

Could someone please share a script for doing this on a bunch of files?

Many thanks Venkat

[venkateshbiotech]

Thank you all for the suggestions

Answer 1

[Pierre Lindenbaum]

something like:

find dir1 dir2 -type f -name "*.fa" |\
   awk '{printf("mv \"%s\" \"%s\"\n",$0,$0);}' |\
   sed 's/\/\([^\/\.]*\)\.[^\/]*$/\/\1\.fa"/' > check_this_script_then_execute.sh

[venkateshbiotech]

Thank you for your quick response, Pierre. Could you please tell me what dir1 dir2 represent in the script? I have used it, but it didn't work.

thanks and regards Venkat

[Pierre Lindenbaum]

https://www.cyberciti.biz/faq/how-to-search-multiple-directories-with-find-command/

[GenoMax]

If your files are in one directory (where you are running this command from) then you do not need to use dir1 dir2 part.

Answer 2

[rpolicastro]

GNU parallel is also an option.

parallel -j1 --dry-run mv {} {= s/\\..+/.fa/ =} ::: *.fa

Remove --dry-run if the commands look good.

You may need to modify the directory structure or regex depending on your actual directory structure and file naming.

Answer 3

[shenwei356]

Also try brename. It's handly and safe, being able to check potential conflicts and errors:

Removing anything after the first dot (-p '\..+' -r "") but without changing the file extension (-e). -R is for rename recursively (including sub directories), and -d is for dry run.

$ brename -R -e -p '\..+' -d
[INFO] search paths: ./
[INFO] 
[INFO] checking: [ ok ] 'GCF_029211165.1_ASM2921116v1_genomic.fa' -> 'GCF_029211165.fa'
[INFO] 1 path(s) to be renamed

Usually, I kept the versions (.1).

$ brename -R -p '^(\w{3}_\d{9}\.\d+).+' -r '$1.fa' -d
[INFO] search paths: ./
[INFO] 
[INFO] checking: [ ok ] 'GCF_029211165.1_ASM2921116v1_genomic.fa' -> 'GCF_029211165.1.fa'
[INFO] 1 path(s) to be renamed