I have multiple unique directories that each contain a file named filtered_feature_bc_matrix.h5. I want to paste the directory-name onto the filename to make the filename unique within each folder. Is this possible?

./sample_scRNA_unsorted_98433_Primary_bam/outs/filtered_feature_bc_matrix.h5
./sample_scRNA_unsorted_77570_Primary_bam/outs/filtered_feature_bc_matrix.h5

out:

./sample_scRNA_unsorted_98433_Primary_bam/outs/sample_scRNA_unsorted_98433_Primary_bam_filtered_feature_bc_matrix.h5
./sample_scRNA_unsorted_77570_Primary_bam/outs/sample_scRNA_unsorted_77570_Primary_bam_filtered_feature_bc_matrix.h5

CodePudding user response：

For completeness here is a solution with only bash built-in:

shopt -s globstar nullglob
name="filtered_feature_bc_matrix.h5"
for f in */**/"$name"; do mv "$f" "${f%/*}/${f%%/*}_$name"; done

CodePudding user response：

find . -type f -name 'filtered_feature_bc_matrix.h5' \
-exec sh -c \
'fp="$1"; d=$(echo "$fp"|cut -d/ -f2); echo $(dirname "$fp")/${d}_$(basename "$fp")' \
-- '{}' \;

• find allows to iterate the files with relative path
• -exec allows to do action on '{}' which is the file path
• sh is used to simplify the action
• dirname and basename allows to extract directories or filename.
• cut is used to extract only the first directory (second field as the first one is .)

To rename:

find . -type f -name 'filtered_feature_bc_matrix.h5' \
-exec sh -c \
'fp="$1"; d=$(echo "$fp"|cut -d/ -f2); mv -v "$fp" "$(dirname "$fp")/${d}_$(basename "$fp")"' \
-- '{}' \;