copy and rename files 2 directory up

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:

#!/bin/bash # 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 IFS=$'\n' # 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 _new_file_path="${_target_directory_path}/${_parent_directory_name}_${_file_name}" echo "${_new_file_path}" # Copy and rename the file echo "cp -i \"${_file_path}\" \"${_new_file_path}\"" cp -i "${_file_path}" "${_new_file_path}" echo done 

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})" done 

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:

#!/bin/bash # create_test_files.bash # Set internal field separator to handle spaces in file names IFS=$'\n' # Choose an prefix for the file paths _prefix="/tmp" # Create array of sample files _sample_files=( "/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam" "/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam" "/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam" ) # Create directories and files for _file in "${_sample_files[@]}"; do # Add the prefix to the path _path="${_prefix}${_file}" # Create parent directory mkdir -p "$(dirname ${_path})" # Create file touch "${_path}" done 

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

$ find /tmp/samples -type f /tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam /tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam /tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam 

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 \ /tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam 

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

$ find /tmp/samples -type f /tmp/samples/mydata1/RUN1/ID_date/PCR2/ID_date_F3.bam /tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam /tmp/samples/mydata2/RUN1/ID2_date4/PCR2/ID2_date4_F3.bam /tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam /tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/IDxxx_datexxx_F3.bam /tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam 

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

find /tmp/samples -type f -exec rm {} \; 

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 dir="${path%/*}" dest="${dir%/*/*}" cp "$path" "${dest}/${dest##*/}_${path##*/}" done 

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) pathtool=realpath # directory levels upwards to copy files levels=2 # iterate over each parameter for path; do if [[ ! $path =~ ^/ ]]; then # convert relative to absolute path="$($pathtool $path)" fi file="${path##*/}" dir="${path%/*}" dest=$dir # chdir upwards 'levels' times to destination for (( i=0; i<$levels; i++ )); do dest="${dest%/*}" done # to be prepended to original filename destpfx="${dest##*/}" newpath="${dest}/${destpfx}_${file}" cp "$path" "$newpath" done 

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 {} + 

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#./}" ' _ '{}' \; 

Explanations::

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.

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 \ /samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam for bam; do dir="$(dirname "$(dirname "$(dirname "$bam")")")" mv "$bam" "$dir"/"$(basename "$dir")"_"$(basename "$bam")" done