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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 OSF1

refile

refile(1)						      General Commands Manual							 refile(1)

NAME

       refile - file message in other folders (only available within the message handling system, mh)

SYNOPSIS

       refile [msgs] [+folder] [options]

OPTIONS

       Refiles	the draft message, or the current message in your +drafts folder, if you have one set up. You cannot give a msgs argument when you
       use this option.  Moves a file into a folder. This option takes a file from its directory and places it in the named folder,  as  the  next
       message	in the folder. The file must be formatted as a legal mail message. This means that the message must have the minimum header fields
       separated from the body of the message by a blank line or a line of dashes.  Prints a list of the valid options to this command.   Keeps  a
       copy  of  the  message in the source folder. Normally, refile removes the messages from the original folder when it refiles them. The -link
       option keeps a copy in the original folder, as well as filing a copy in the new folder.	Preserves the number  of  a  message  in  the  new
       folder.	Normally,  when  a  message  is refiled in to another folder, it is set to the next available number in that folder. The -preserve
       option keeps the number of the message the same in the new folder as it had been in the old.

	      You cannot have two messages with the same number in one folder, so you should use this option  with  care.   Specifies  the  source
	      folder to take messages from. Normally, messages are refiled from the current folder into another folder. However, you can take mes-
	      sages from a different folder by using the -src +folder option to specify the alternative source folder.

DESCRIPTION

       Use the refile command to move the specified message from the current folder to another folder. You can refile messages in  more  than  one
       folder by giving multiple folder names as arguments.

       If you do not specify a message, the current message is refiled. You can refile a message other than the current message by giving its num-
       ber as a msgs argument. You can also refile more than one message at a time by specifying more than one message number, or a range of  mes-
       sage numbers, or a message sequence. See mark(1) for more information on sequences.

       The  current  folder  remains  the same unless the -src option is specified; in that case, the source folder becomes current. Normally, the
       last message specified becomes the current message. However, if the -link option is used, the current message is not changed.

       If the Previous-Sequence: entry is set in the file, in addition to defining the named sequences from the source folder,	refile	will  also
       define those sequences for the destination folders. See mh_profile(4) for information concerning the previous sequence.

PROFILE COMPONENTS

       Path: To determine your Mail directory

       Folder-Protect: To set protections when creating a new folder

       rmmproc: Program to delete the message

EXAMPLES

       The  following  example	refiles  messages 3 and 5 in the folder +records: % refile 3 5 +records The next example files the current message
       into two folders: % refile +jones +map The next example takes message 13 in the current folder and refiles it in the +test folder. The mes-
       sage remains in the current folder as well as appearing in the +test folder.  % refile -link 13 +test The next example takes a message from
       the folder +test when it is not the current folder, and places it in the folder +outbox: % refile 3 -src +test +outbox

FILES

       The user profile.

SEE ALSO

       folder(1), mark(1), mh_profile(4)

																	 refile(1)
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