I am using ubuntu 14.04 as my os.
Each .bam and .bam.bai is inside each R_2019 directory but it looks like the files can not be found. Thank you .
set -xv
Code:
ROOTDIR=/home/cmccabe/rename
ROOTDIR=/home/cmccabe/rename
+ ROOTDIR=/home/cmccabe/rename
cmccabe@Satellite-M645:~$ cd $ROOTDIR || exit 1
cd $ROOTDIR || exit 1
+ cd /home/cmccabe/rename
cmccabe@Satellite-M645:~/rename$ # matching name "R_2019*" to operate on desired directory names, expand this to be precise.
# matching name "R_2019*" to operate on desired directory names, expand this to be precise.
cmccabe@Satellite-M645:~/rename$ MDIR="R_2019*"
MDIR="R_2019*"
+ MDIR='R_2019*'
cmccabe@Satellite-M645:~/rename$ find . -mindepth 1 -maxdepth 1 -type d -name "${MDIR}" | while read RDIR
find . -mindepth 1 -maxdepth 1 -type d -name "${MDIR}" | while read RDIR
> do
do
> TRIMSTR="${RDIR%%-v5.6*}"
TRIMSTR="${RDIR%%-v5.6*}"
> for FLN in $RDIR/*.bam $RDIR/*.bam.bai
for FLN in $RDIR/*.bam $RDIR/*.bam.bai
> do
do
> FLNSUB="_${RDIR/\.\//}"
FLNSUB="_${RDIR/\.\//}"
> "mv ${FLN} ${FLN/$FLNSUB}"
"mv ${FLN} ${FLN/$FLNSUB}"
> done
done
> # Now we shall rename the folder, after files inside have been renamed.
# Now we shall rename the folder, after files inside have been renamed.
> "mv $RDIR ${TRIMSTR}"
"mv $RDIR ${TRIMSTR}"
> done
done
+ read RDIR
+ find . -mindepth 1 -maxdepth 1 -type d -name 'R_2019*'
+ TRIMSTR=./R_2019_01_30_14_24_53_user_S5-0271-95
+ for FLN in '$RDIR/*.bam' '$RDIR/*.bam.bai'
+ FLNSUB=_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
+ 'mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx.bam'
bash: mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx.bam: No such file or directory
+ for FLN in '$RDIR/*.bam' '$RDIR/*.bam.bai'
+ FLNSUB=_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
+ 'mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx.bam'
bash: mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx.bam: No such file or directory
+ for FLN in '$RDIR/*.bam' '$RDIR/*.bam.bai'
+ FLNSUB=_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
+ 'mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx.bam.bai'
bash: mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx.bam.bai: No such file or directory
+ for FLN in '$RDIR/*.bam' '$RDIR/*.bam.bai'
+ FLNSUB=_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
+ 'mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx.bam.bai'
bash: mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx.bam.bai: No such file or directory
+ 'mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions ./R_2019_01_30_14_24_53_user_S5-0271-95'
bash: mv ./R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions ./R_2019_01_30_14_24_53_user_S5-0271-95: No such file or directory
+ read RDIR
--- Post updated at 08:01 AM ---
@Don Cragun I just tried the scrip by @Peasent and posted the results. The files could not be found to trim. I am using ubuntu 14.04 currently and may be migrating to centos 7 in the near future.
I do have backups of the data and removed the echo as the output looked correct and since Ihave backups I performed the mv. As I look back it was not correct but the .bam files were trimmed as expected it was the .bam.bai that were not. Thank you .
Code:
find /home/cmccabe/rename/ \( -type d -o -name '*.bam*' \) -exec ls -ld {} +
drwxrwxr-x 3 cmccabe cmccabe 4096 Mar 17 07:28 /home/cmccabe/rename/
drwxrwxr-x 2 cmccabe cmccabe 4096 Mar 17 07:34 /home/cmccabe/rename/R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
-rw-rw-r-- 1 cmccabe cmccabe 0 Feb 28 14:59 /home/cmccabe/rename/R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam
-rw-rw-r-- 1 cmccabe cmccabe 0 Feb 28 14:59 /home/cmccabe/rename/R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_011_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai
-rw-rw-r-- 1 cmccabe cmccabe 0 Feb 28 14:59 /home/cmccabe/rename/R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam
-rw-rw-r-- 1 cmccabe cmccabe 0 Feb 28 14:59 /home/cmccabe/rename/R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions/xxx_013_xx00_xxx_R_2019_01_30_14_24_53_user_S5-0271-95-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions.bam.bai
Last edited by cmccabe; 03-17-2019 at 10:04 AM..
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