Bash to trim folder and files within a path that share a common file extension
The bash will trim the folder to trim folder. Within each of the folders (there may be more than 1) and the format is always the same, are several .bam and matching .bam.bai files (file structure) and the bashunder that executes and trims the .bam as expected but repeats the.bam.bai extentions after trimming those files. xxxx_0113_xxx_xxx.bam.bai.bam.bai also in the set -xv. I think the .bam extension common to both may be causing the repeat but am not sure. Removing the .bam.bai from the mv did not fix the repeats. The end goal is to trim the folders and the files within each of the folders and I am not sure if the nested loops are the best way (probably not). Thank you .
bash to trim folder
Code:
for folder in /home/cmccabe/rename/*/ ; do ## start loop in subdirectory
mv "$folder" "${folder%%-v5.6*}" ## trim folder name
done ## close loop
for d in /home/cmccabe/rename/* ; do ## start loop in parentdir
if [ -d "$d" ]; then ## grab subdir and store in parentdir/subdir in $d
subdir="$(basename $d)" ## define sub-directory
fi ## end if
for bam in "${d}"/*.bam ; do ## iterate through each file in parentdir and read into bam
for bai in "${d}"/*.bam.bai ; do ## iterate through each file in parentdir/subdir and read into bai
bam_path_removed=$(echo $bam| awk -F/ '{print $NF}') ## cut text before last /
bai_path_removed=$(echo $bai| awk -F/ '{print $NF}') ## cut text before last /
bam_trim=$(echo "$bam_path_removed"|cut -f1,2,3,4 -d'_')
bai_trim=$(echo "$bai_path_removed"|cut -f1,2,3,4 -d'_')
mv "${bam}" "${d}/${bam_trim}".bam ## rename all bam
mv "${bai}" "${d}/${bai_trim}".bam.bai ## rename all bai
done ## close loop
done ## close loop
done ## close loop
Dear Chaps,
What will I do if, I am not sure about the length of the file name, but only one thing that I want to remove only the last extension.
e.g. abcdXXXXXX.pqrXXXXX.asc (X is any character)
I want to trim only .asc (or,watever) so that resultant file name would be like... (1 Reply)
Hello,
I am an amature at UNIX commands and functionality.
Please could you all assist me by replying to my below mentioned querry :
How can I upload a zip folder on a unix path from my windows folder?
Thanks guys
Cheers (2 Replies)
Hi,
I need command to display files with full path and date of files where are generated at every 5hrs in a folder.
eg:
/u01/app/test/orjthsd_1_1 Sun May 10 19:03:26 2009
/u01/app/test/weoiusd_1_1 Sun May 10 21:00:26 2009
thanks
saha (3 Replies)
I have the following files in the dir /home/krishna/datatemp
abc.xml
cde.xml
asfd.txt
asdf_20120101-1.xml
asdf_20120101-2.xml
asdf_20120101-3.xml
asdf_20120101-4.xml
Now I need to move the files having the pattern asdf_20120101-*.xml to the dir /home/krishna/dataout with the extn as... (1 Reply)
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Can you please provide some pointers to move files from Base path to multiple paths in efficient way.Folder Structure is already created.
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Hi
I have a requirement like this:
/abc/a/x.txt
/abc/a/y.txt
/abc/b/x.gz
/abc/b/y.txt
I need output like this:
/abc/a:*.txt
/abc/b:*.txt
/abc/b:*.gz
I have tried find /abc -type f -name "*.*" ||awk -F . '{print $NF}' it is print only extensions without path name.
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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)
03-16-2019
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