The bash below executes and does find all the .bam files in each R_2019 folder. However set -x shows that the .bam extension only gets removed from one .bam file in each folder (appears to be the last in each). Why is it not removing the extension from each (this is $SAMPLE)? Thank you .
Code:
set -x
DIR=/home/cmccabe/Desktop/f1 ## define data directory path
for RDIR in "$DIR"/R_2019* ; do
BAM=$(find "$RDIR"/bam -type f -name "*.bam" -printf '%P\n')
SAMPLE=$(echo $BAM|cut -d. -f1)
echo "$SAMPLE"
done
I think you could spare yourself a lot of hassle (and the system a lot of work) doing it like this:
Code:
for RDIR in "$DIR"/R_2019* ; do
find "$RDIR"/bam -type f -name "*.bam" -exec /path/to/movescript.sh {} \;
done
where /path/to/movescript.sh would contain
Code:
!# /bin/sh
echo mv "${1}" "${1%.bam}"
exit $?
If you are satisfied with the list of commands remove the "echo" in the script.
Hi ALL,
I'm new to this forum.
Thanks and congrats to all for their great efforts building this site simply superb for all unix administrators.
My requirement is to remove extensions of the files in the current directory. I'm doing it using below script which is working but i think it is... (12 Replies)
Here's the story:
I have two txt files of filenames one is like this
W00CHZ0103340-I1CZ31
W00CHZ0103340-I1CZ32
W00CHZ0103340-I1CZ33
W00CHZ0103341-I1CZ35
W00CHZ0103342-I1CZ46
W00CHZ0103343-I1CZ37
W00CHZ0103344-I1CZ39
W00CHZ0103345-I1CZ43
W00CHZ0103345-I1CZ44
...
the other like this
... (5 Replies)
hello
i have 2 question
if i have 1 folder and under this folder many many sub folders and in every folders many files with man extension like *php * jpg * gif
i need to remove all *php files
1- from tha main folder only
2- from tha main folder and all sub folders
the second how... (6 Replies)
There are few files in my windows directory and I need a perl script to rename the files to its original names i.e., the last extension(.orig) needs to be removed programatically,
files in directory
data1.htm.orig
data2.htm.orig
data3.htm.orig
to be renamed to
data1.htm
data2.htm... (4 Replies)
Hi,
I have some files with some extension e.g. abc.xml.REMOVE,xyz.xml,efg.xml.REMOVE .
I have to remove the .REMOVE extension. I can display it using the below script but cannot rename it.
ls -l|sed 's/\.REMOVE//'
How can I rename this?
Thanks in advance (7 Replies)
Hi all
i am new for the shell scripting can any one help me with my requirments . i want to delete file older than 21 days everything works fine but in that dir i got the files with should not be deleted with particular extension like (.info):confused:here is the script i wrote .can anyone... (5 Replies)
hi,
i have a directory which contains some files and a subdirectory. i am writing only the files names to a file using the below code.
ls -ltr | grep "^-" | awk '{print $NF}' > /home/file_list$$
cat /home/file_list$$
s1_abc.txt
s2_def.xls
s3_def.xls
as you can see there is one .txt... (7 Replies)
how can i remove numbers of characters from the last name of file with respect to not remove the files extension
example
VFX_Official_Trailer_(HD)__Shhh__-_by_Freddy_Chavez_Olmos_&_Shervin_Shoghian-.mp4
i want to rename this to
VFX-Official-Trailer-(HD)-Shhh... (13 Replies)
Dear all
sorry for bothering you wityh dumb question but I am stucked with an issue.
Well, I am trying to loop over files in folder, make an operation and rewrite the output.
Example:
INPUT
file1.txt
file2.txt
file3.txtMy command (doesn't work!!)
for file in /path/to/*.txt
do command... (13 Replies)
In the bash below I am trying to create sub-directories inside a directory from files with specific .bam extensions. There may be more then one $RDIR ing the directory and the .bam file(s) are trimmed (removing the extension and IonCode_0000_) and the result is the folder name that is saved in... (2 Replies)
03-29-2019
.