[SOLVED] Bash: Reposition substring within a string

Issue

I have some files which I would like to rename. The filenames look like below:

C18-02B-NEB-sktrim_1-20000000.fq
C18-02B-NEB-sktrim_1-30000000.fq
C18-02B-NEB-sktrim_1-50000000.fq
C18-02B-NEB-sktrim_2-20000000.fq
C18-02B-NEB-sktrim_2-30000000.fq
...

I would like to reposition the _digit part to before .fq like so.

C18-02B-NEB-sktrim-20000000_1.fq
C18-02B-NEB-sktrim-30000000_1.fq
C18-02B-NEB-sktrim-50000000_1.fq
C18-02B-NEB-sktrim-20000000_2.fq
C18-02B-NEB-sktrim-30000000_2.fq
...

I am able to capture my substring of interest as such:

find  * | egrep -o '_[0-9]'
_1
_1
_1
_2
_2

I could also remove the substring from the string as such:

find  * | sed 's/_[0-9]//'
C18-02B-NEB-sktrim-20000000.fq
C18-02B-NEB-sktrim-30000000.fq
C18-02B-NEB-sktrim-50000000.fq
C18-02B-NEB-sktrim-20000000.fq

but I am not sure how to move it over to the new position and then rename the files.

Solution

This should do it:

find . -name '*.fq' -exec sh -c 'mv "$0" "$(echo "$0" |sed "s/^\(.*\)\(_[0-9]\)\(.*\)\.fq$/\1\3\2.fq/")"' {} \;

sed part:

sed "s/^\(.*\)\(_[0-9]\)\(.*\)\.fq$/\1\3\2.fq/"

Explanation:

find . -name '*.fq' searches for the glob pattern *.fq and then the -exec option executes a mv command per each file found.

The sh -c 'mv "$0" "$var"' {} construct is just a mv command with two arguments and $0 is substituted with {} which is the filename found by find

---

If file renaming is all you want, better use tools that are exclusively for file renaming though. rename is a pretty popular tool to do this kind of stuff, but I got my own tool: [rnm][1].

With rnm, you can do:

rnm -rs '/^(.*)(_\d)(.*)\.fq$/\1\3\2.fq/' *.fq

Or using the exact same regex like the sed command (i.e BRE): BRE support was dropped in favor of PCRE2.

Answered By - Jahid

Answer Checked By - Marilyn (WPSolving Volunteer)