same file name in multiple directories: how to assign them with different names at the same time with only one command?

Question

I have 23 different directories and in each one of them I have a file called accepted_hits.bam

so I need to generate a unique name in each directory: e.g accepted_hits.bam_1 for directory 1 accepted_hits.bam_2 for directory 2

and so on 23 times. Is there a easy way to do that with a single command?

Answer 1

With bash and find

find . -type f -name accepted_hits.bam -exec bash -c \
'i=0; for f; do (( ++i )); mv -- "$f" "${f}_$i"; done' _ {} +

Answer 2

Assuming your directories are all at the same parent, try this:

$ for f in $(ls */accepted_hits.bam); do mv $f $(dirname $f)/$(dirname $f)-$(basename $f); done

Answer 3

I would probably use awk, but that's just a matter of taste, not of right and wrong:

find . -name accepted_hits.bam | awk '{ print "cp -pi \"" $0 "\" \"" $0 "\"_" NR "; mv -i \"" $0 "\"_" NR " ./bam-files/" }' | tcsh -f

where you need to create a directory ./bam-files/ before calling above line, or adjust the directory name. I have intentionally used -p for preserving file times and -i for avoiding overwrites, just in case. So, before calling the commands for a 2nd time please clean the target directory.

If you wish to remove the original files please replace the cp -pi by mv -i.

The script leaves out calls to basename in the hope to run into less trouble if the pathname contains special characters (spaces and most special characters are handled).

PS: You could also do a dry-run before executing by leaving out the | tcsh -cf at the end. If you do not have tcsh installed (yes, there are Linuxes without it) feel free to use sh or bash.

Answer 4

If you would just like to name them as unique files, you can use the RANDOM variable as below:

find /basedir/ -type f -name "accepted_hits.bam" -exec bash -c 'mv $0 $0.$RANDOM' {} +

If you would like to sequentially name them, you can append a counter value at the end of the filename as below:

for file in $(find /basedir/ -type f -name "accepted_hits.bam"); do ((count++)) ; mv $file ${file}_${count}; done

The above two methods rename the file in the same directory. If you'd like to rename them to a different directory, you can combine them with @schlimmchen's answer ( using basename and dirname ). You can even insert an echo statement before the move command to see the result without actually moving the files. I've found it a handy way to test the commands without risking any changes to the files.

Answer 5

This is very easy do to with shell globs:

1. Add a counter to the name (accepted_hits.bam.1, accepted_hits.bam.2 and so on):

   c=0; for f in */accepted_hits.bam; do mv "$f" "$f".$((++c)); done
   

   Explanation

   This simply iterates over all files called accepted_hits.bam that are in subdirectories of the current directory, and saves each of them as $f. The $((++c)) construct increments a counter ($c), so $f.$((++c)) will be file.1, file.2 etc, incremented on each iteration.

   Note that I am using c=0 at the beginning. If you don't do this, subsequent runs will keep the value of $c and it will keep incrementing.

2. Add a counter but before the extension (accepted_hits.1.bam, accepted_hits.2.bam and so on):

   c=0; for f in */accepted_hits.bam; do  
       mv "$f" "$(dirname "$f")"/"$(basename "$f" .bam)".$((++c)).bam
   done
   

   Explanation

   The command dirname returns the path to a file's parent directory:

   $ dirname /usr/local/bin/apt 
   /usr/local/bin
   

   The command basename is the inverse, it removes the directory, leaving only the last part of the path and can also remove an extension:

   $ basename /etc/apt/sources.list
   sources.list
   $ basename /etc/apt/sources.list .list   ## remove extension
   sources
   

   So, mv "$f" "$(dirname "$f")"/"$(basename "$f" .bam)".$((++c)).bam will rename the file as desired.

3. Add the parent directory's name (accepted_hits.dir1.bam, accepted_hits.dir2.bam, or whatever your directory names are)

   for f in */accepted_hits.bam; do  
       dir="$(dirname "$f")"; mv "$f" "$dir"/"$(basename "$f" .bam)"."$dir".bam
   done
   

   Explanation

   This is the same idea as above, only I am saving the directory's name as a variable to simplify using it as part of the file name.

4. Use external tools. Perl rename for example. The standard rename that ships with Debian-based distributions can't deal with incrementing counters. However, I found this one which can. Download the script linked to in that page, save it as increname in your current directory and run it like this:

   perl increname -n 's/.bam/++$c . ".bam"/e' */accepted_hits.bam