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Full Discussion: Bash to trim folder and files within a path that share a common file extension
Top Forums Shell Programming and Scripting Bash to trim folder and files within a path that share a common file extension Post 303032427 by Don Cragun on Sunday 17th of March 2019 01:59:58 PM
Old 03-17-2019
Hi Peasant,
Here is a slightly modified version of your script that just uses options and variable expansions defined by the POSIX standards. But, of course, it still depends on us knowing the pathname of a shell that provides those standard variable expansions. (Note that find isn't needed for this; we can get what we need just using shell pathname expansions.)
Code:
#!/bin/bash
set -xv
# we are running this from ROOTDIR, or abort.
ROOTDIR=/home/cmccabe/rename
cd $ROOTDIR || exit 1
# matching name "R_2019*" to operate on desired directory names, expand this to be precise.

for RDIR in R_2019*/
do
	TRIMSTR=${RDIR%%-v5.6*}
	for FLN in $RDIR*.bam	# Note that RDIR contains a trailing /.
	do
		FLNSUB=${FLN%_R_2019_*}
		mv "${FLN}" "$FLNSUB.bam"
		# Use the fact that .bam and .bam.bai files are paired.
		mv "${FLN}.bai" "$FLNSUB.bam.bai"
	done
	# Now we shall rename the folder, after files inside have been renamed.
	mv "$RDIR" "${TRIMSTR}"
done

Hi cmccabe,
If Peasant's script (modified as suggested in post #5 worked for you, the script above should also work and should even run a little bit faster since it doesn't need to invoke find to get the job done.

I hope this helps,
Don
These 2 Users Gave Thanks to Don Cragun For This Post:
cmccabe Peasant
 

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LEARN ABOUT LINUX

dbs-edit-patch

DBS-EDIT-PATCH(1)                                               Debian Build System                                              DBS-EDIT-PATCH(1)

NAME

       dbs-edit-patch - Edit a DBS patch

SYNOPSIS

       dbs-edit-patch [options] patch
       dbs-edit-patch -h|--help

DESCRIPTION

       dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format.

WARNING

       dbs  is  deprecated,  please  switch  to  the  `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb-
       Src3.0#FAQ for a short guide how to do it.

OPTIONS

       -h, --help
              Show summary of options.

       -t dir, --tmpdir=dir
              Directory for the temporary files, default is /tmp or if set $TMP.

       -s dir, --sourcedir=dir
              Top level directory of the debian-package source-tree, default is the present working directory.

       -P dir, --sourcepatchdir=dir
              Directory containing upstream patches.

       -T dir, --sourcetardir=dir
              Directory containing the upstream tarball.

       -p level, --strip=level
              Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0.

ENVIRONMENT VARIABLES

       TMP    Sets the directory for the temporary files, can be overridden with -t dir.

debian/vars
       dbs-edit-patch will automatically use variables defined in the optional debian/vars file.

       When a file debian/vars.in exists and debian/vars either does not exist or is older  than  any  of  the  following  files:  debian/vars.in,
       debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command
           make -f debian/rules -W debian/vars.in debian/vars

EXAMPLES

       Edit the 021_debian patch of Heimdal:

           ~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian
           Extracting source heimdal-0.3d.tar.gz ... successful.
           Applying patch 001_replay ... successful.
           etc.
           Copying heimdal-0.3d to heimdal-0.3d-old ... successful.
           Applying patch 021_debian ... successful.

       Edit  files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired,
       and finally execute /tmp/021_debian/dbs-update-patch to save the results.

       Technical  note:  dbs-edit-patch  extracts  all  patches  before  021_debian  into  /tmp/021_debian/heimdal-0.3d,  copies  the  result   to
       /tmp/021_debian/heimdal-0.3d-old,  and  applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create
       the diff between the old and new directories:

           ~/heimdal-0.3d> ls -la /tmp/021_debian
           total 12
           -rwxr-xr-x    1 bam      users         112 Jan 31 13:31 dbs-update-patch*
           -rw-r--r--    1 bam      users           0 Jan 31 13:31 patch-description
           drwxr-xr-x   14 bam      users        4096 Jan 31 13:31 heimdal-0.3d/
           drwxr-xr-x   14 bam      users        4096 Jan 31 13:31 heimdal-0.3d-old/
           drwxr-xr-x    5 bam      users        4096 Jan 31 13:31 .stampdir/

           ~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch
           #!/bin/sh -e
           cd "/tmp/021_debian"
           HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks"
           test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff
           find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm
           find -name "*~" -print0 | xargs -0 --no-run-if-empty rm
           : > new_patch
           test ! -e patch-description || cp patch-description new_patch
           diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1
           mv new_patch  /usr/src/heimdal/debian/patches/021_debian
           test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff

SEE ALSO

       diff(1), dbs(7), /usr/share/doc/dbs/

AUTHOR

       DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by  Brian  May.  This  manpage  was  generated  by
       Andreas Metzler and modified by Robert Luberda.

Debian                                                          February 15th, 2011                                              DBS-EDIT-PATCH(1)
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