[SOLVED] bash: operation with the filles according two different patterns

Issue

my bash script looks within the $dir any *.pdb filles which starts with the $mask keyword and then copy them to the $target_dir

mask1='MD_' #usually suffix
mask2='_after_equil' #usually posfix before the pdb extension
    find "$dir" -maxdepth 2 -name "${mask1}*A.pdb" -exec cp {} ${target_dir} \; # 

I would like to modify this script adding the IF condition in the following manner: if the pdb files with the $mask1 are not found in the $dir instead to look for the pdb files with the $mask2, then remove the $mask2 from the name of each file and add the $mask1 in the begining, and finally copy the renamed pdb files to the targer dir:

e.g this the following filles should be processed:

1rep_6nax_apo_300K_after_equil.pdb  3rep_6nax_apo_300K_after_equil.pdb
2rep_6nax_apo_300K_after_equil.pdb  4rep_6nax_apo_300K_after_equil.pdb

that should be renamed to

MD_1rep_6nax_apo_300K.pdb  MD_3rep_6nax_apo_300K.pdb
MD_2rep_6nax_apo_300K.pdb  MD_4rep_6nax_apo_300K.pdb

and then coppied to $target_dir

Solution

First 3 lines same as in your question (but quoting target_dir) and then add a loop to do the rest:

mask1='MD_' #usually suffix
mask2='_after_equil' #usually posfix before the pdb extension
find "$dir" -maxdepth 2 -name "${mask1}*A.pdb" -exec cp {} "$target_dir" \; 

while IFS= read -d '' -r old; do
    file="${old##*/}"
    new="${target_dir}/${mask1}${file%${mask2}.pdb}.pdb"
    cp -- "$old" "$new"
done < <(find "$dir" -maxdepth 2 \( -name "*${mask2}.pdb" -a ! -name "${mask1}*A.pdb" \) -print0)

Answered By - Ed Morton

Answer Checked By - David Marino (WPSolving Volunteer)