find

Loop over all files in all sub-directories


# show all .fasta files in all sub-directories of folder 'assembly'
find assembly/ -name "*.fasta"
assembly/projectA/run1.fasta
assembly/projectA/run2.fasta
assembly/projectB/run1.fasta
assembly/projectB/run2.fasta
assembly/final.fasta


# search for 'plasmid' in all fasta files (run command  grep  on all files) in folder 'assembly'
find assembly/ -name "*.fasta" -exec grep --with-filename plasmid {} \;


# compress all .fasta files using gzip, include all sub-directories of folder 'assembly'
find assembly/ -name "*.fasta" -exec gzip {} \;

General


find /path/ -name   filter files   -exec   run command         {} \;

  -name  # filter filenames
  -exec  # run command
   {}    # on each file
   \;    # pass files one by one to the command



https://help.ubuntu.com/community/find