I am trying to copy multiple files named "F3.bam" two level of directories to up and then rename these files with the name of the sub-directory after copy.

For example:


Expected results:

1. The files are first copied two directories level up:


2. The files are renamed according to the name of the current sub-directory:


Ideally a bash loop would be great (working on a Mac).


Here's the TLDR version of my solution: you can use the dirname and basename commands along with process substitution in order to construct the target path for your copy command.

A longer explanation follows.

Here is a (super verbose) script that does roughly what you want using a Bash loop:


# copy_and_rename.bash
#   Copy multiple files 2 folders up and rename these files
#   to contain their parent directory as a prefix.

# Set internal field separator to handle spaces in file names

# Iterate over the list of file paths
for _file_path in $@; do

    # Get the file name
    _file_name="$(basename ${_file_path})"

    echo "${_file_name}"

    # Get the path to the target directory (two levels above the file)
    _target_directory_path=$(dirname $(dirname ${_file_path}))

    echo "${_target_directory_path}"

    # Get the parent directory of the target directory
    _parent_directory_path=$(dirname ${_target_directory_path})

    echo "${_parent_directory_path}"

    # Get the name of the parent directory
    _parent_directory_name=$(basename ${_parent_directory_path})

    echo "${_parent_directory_name}"

    # Construct the new file path

    echo "${_new_file_path}"

    # Copy and rename the file
    echo "cp -i \"${_file_path}\" \"${_new_file_path}\""
    cp -i "${_file_path}" "${_new_file_path}"

You can obviously compress this a lot, but I kept it this way for explanatory value.

Here is what the preceding script looks like without any comments or superfluous variables or echo statements:

for _file_path in $@; do
    cp -i "${_file_path}" \
    "$(dirname $(dirname ${_file_path}))/$(basename $(dirname $(dirname $(dirname ${_file_path}))))_$(basename ${_file_path})"

It's very fragile and doesn't do much in the way of error-handling. I also left in some echo statements for debugging so you see what it's doing and can sanity-check it when you run it for the first time.

To test it I created your files by using the following script, which I include here in case you find it useful for further testing:


# create_test_files.bash

# Set internal field separator to handle spaces in file names

# Choose an prefix for the file paths

# Create array of sample files

# Create directories and files
for _file in "${_sample_files[@]}"; do

    # Add the prefix to the path

    # Create parent directory
    mkdir -p "$(dirname ${_path})"

    # Create file
    touch "${_path}"

I check that the files were created properly by using the find command:

$ find /tmp/samples -type f


Then I invoke the script like this:

bash copy_and_rename.bash \
/tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam \
/tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam \

And then I check that the script worked by using find again:

$ find /tmp/samples -type f


Finally, I delete all of the test files, also using find:

find /tmp/samples -type f -exec rm {} \;
| improve this answer | |
  • That looks very promising! I will give it a try asap and keep you posted – antoine Oct 16 '17 at 1:56

This version uses only bash parameter substitution to slice and dice paths. Pass it one or more absolute file paths:

#!/bin/env bash
for path; do
    cp "$path" "${dest}/${dest##*/}_${path##*/}"

Here is an expanded version. This one also accepts relative paths and the number of parent dirs to traverse is tunable:

#!/bin/env bash

# Each param for this script is the path of a file. It
# accepts relative paths if you have appropriate tool to
# robustly determine absolute paths (not trivial). Here
# we're using GNU 'realpath' tool.
# Usage: copy2up filepath1 [filepath2...]

# for converting relative paths to absolute
# if it's missing replace realpath with available tool
# (or just always use absolute path arguments)

# directory levels upwards to copy files

# iterate over each parameter
for path; do
    if [[ ! $path =~ ^/ ]]; then
        # convert relative to absolute
        path="$($pathtool $path)"

    # chdir upwards 'levels' times to destination
    for (( i=0; i<$levels; i++ )); do

    # to be prepended to original filename

    cp "$path" "$newpath"

As for your specific use case, you could run this with find if that's how you are locating your 'F3.bam' files. For example:

find /some/path -name F3.bam -exec copy2up.sh {} +
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Using find and shell (POSIX sh/bash/Korn/zsh) parameter substitution expansion as following.

find . -type f -name "F3.bam" -execdir sh -c '
    trgt="${PWD%/*/*}"; echo cp -v "$1" "${trgt}/${trgt##*/}_${1#./}" ' _ '{}' \;


We are looking for the files only matching F3.bam and with -execdir here, find is changing the current directory to the directory where file F3.bam found then execute the sh -c ' ... ' within that directory itself.

With trgt="${PWD%/*/*}" "cut-up-to-first-suffix": We are getting ride of the filename itself and two level of its sub-directories in /samples/mydata1/RUN1/ID_date**/PCR2/TIME1** (bold part that matches /*/* suffix will remove) and assign to variable trgt. So trgt is now set to /samples/mydata1/RUN1/ID_date for first file.

The "$1" is relative filepath ./filename to the current $PWD.

In ${trgt##*/}_ "cut-up-to-last-prefix": We used trgt variable value to get the sub-directory name which should pre-pend to the filename, So this will return only ID_date, ID2_date4 or IDxxx_datexxx, etc (removing everything until last slash / seen) and add a underscore _.

This ${1#./} removes point-slash ./ from the relative ./filepath.

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You can nest dirname as often as you like:

set /samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam \
/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam \

for bam; do
  dir="$(dirname "$(dirname "$(dirname "$bam")")")"
  mv "$bam" "$dir"/"$(basename "$dir")"_"$(basename "$bam")"
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