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
What you have shown us above makes it look like you may have moved a bunch of your *.bam.bai files into *.bam.bai.bam.bai files and possibly moved *.bam files into *.bam.bam files. The purpose of the echo commands was to make sure that the mv commands that would be executed looked good before actually moving files. The fact that the echoset -xv output did not show the same filenames as the mvset -xv output seems to imply that when the echo was removed from the echo mv lines in your script, something else in your script was changed than just removing the echo in front of the two mv commands.
Since the output from the set -xv trace showed that it was going to rename files in the wrong directory, why did you remove the echo and run it again? The purpose of having the echo in there is so that you can verify that the command being echoed is the command that you want the script to actually perform when run a second time with the echos removed.
Please show us the output from the command:
Code:
find /home/cmccabe/rename/ \( -type d -o -name '*.bam*' \) -exec ls -ld {} +
so we can see how things stand now. Please also tell us what operating system you're using. (PLEASE always tell us what operating system and shell you're using when you start a new thread.)
I don't know if you have tried running the code Peasant suggested in post #2 in this thread. I'm afraid the code Peasant suggested might only work with the file hierarchy you described before any files were moved. (Note that I haven't tried to figure out what his code will do if it starts with your modified file hierarchy instead of what may be the current file hierarchy.) Do you have backups so you can restore that original state? If not, I'm hoping that with the output from the find command above we'll be able to find a way to get to where you want to be without losing any data.
This User Gave Thanks to Don Cragun For This Post:
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