Loop over all files in all sub-directories
# show all .fasta files in all sub-directories of folder 'assembly'
# search for 'plasmid' in all fasta files (run command find assembly/ -name "*.fasta" assembly/projectA/run1.fasta assembly/projectA/run2.fasta assembly/projectB/run1.fasta assembly/projectB/run2.fasta assembly/final.fasta 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 {} \; find /path/ -name filter files -exec run command {} \; -name # filter filenames -exec # run command {} # on each file \; # pass files one by one to the commandhttps://help.ubuntu.com/community/find |