Question

I need a Bash Script to Execute a program for all directories that do not have a specific file and create the output file on the same directory.This program needs an input file which exist in every directory with the name *.DNA.fasta.Suppose I have the following directories that may contain sub directories also

dir1/a.protein.fasta  
dir2/b.protein.fasta  
dir3/anyfile  
dir4/x.orf.fasta

I have started by finding the directories that don’t have that specific file whic name is *.protein.fasta
in this case I want the dir3 and dir4 to be listed (since they do not contain *.protein.fasta)
I have tried this code:

find . -maxdepth 1  -type d  \! -exec test -e '{}/*protein.fasta' \; -print

but it seems I missed some thing it does not work.
also I do not know how to proceed for the whole story.

Answer 1

This is a tricky one.

I can’t think of a good solution. But here’s a solution, nevertheless. Note that this is guaranteed not to work if your directory or file names contain newlines, and it’s not guaranteed to work if they contain other special characters. (I’ve only tested with the samples in your question.)

Also, I haven’t included a -maxdepth because you said you need to search subdirectories too.

#!/bin/bash

# Create an associative array
declare -A excludes

# Build an associative array of directories containing the file
while read line; do
  excludes[$(dirname "$line")]=1
  echo "excluded: $(dirname "$line")" >&2
done <<EOT
$(find . -name "*protein.fasta" -print)
EOT

# Walk through all directories, print only those not in array
find . -type d \
| while read line ; do
  if [[ ! ${excludes[$line]} ]]; then
    echo "$line"
  fi
done

For me, this returns:

.
./dir3
./dir4

All of which are directories that do not contain a file matching *.protein.fasta. Of course, you can replace the last echo "$line" with whatever you need to do with these directories.

Alternately:

If what you’re really looking for is just the list of top-level directories that do not contain the matching file in any subdirectory, the following bash one-liner may be sufficient:

for i in *; do test -d "$i" && ( find "$i" -name '*protein.fasta' | grep -q . || echo "$i" ); done