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Rename not executing in centos 7 as expected

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# 1  
Rename not executing in centos 7 as expected

In the rename below the /path/to/folder... is trimmed (an example is in the parenthesis. Each .bam and .bam.bai in that trimmed directory in the bam sub-folder is then renamed by removing the IonCode_0000_ in the beginning of each filename, leaving just the unique id. The files are always in pairs that is there will always be a matching .bam and .bam.bai. The code executes correctly in ubuntu 14.04 but not in centos 7 as the files do not get renamed to the desired. I am not sure what is different as the rename utility is there in centos 7. The command does execute but the rename does not happen and the file is unchaged. Thank you Smilie.


IonCode_0000_16-1111-Last,First.bam             IonCode_0001_17-0000-L,F-REPEAT.bam
IonCode_0000_16-1111-Last,First.bam.bai         IonCode_0001_17-0000-L,F-REPEAT.bam.bai

mv "$RDIR" "${TRIMSTR}"  ## trim folder name to (/path/to/folder/R_2019_xx_xx_xx_xx_xx_yyyy_X1-0000-101) --- this is "$TRIMSTR" ---
     rename s/"IonCode_[0-9][0-9][0-9][0-9]_"/""/g "$TRIMSTR"/bam/*.bam
     rename s/"IonCode_[0-9][0-9][0-9][0-9]_"/""/g "$TRIMSTR"/bam/*.bam.bai


16-1111-Last,First.bam             17-0000-L,F-REPEAT.bam
16-1111-Last,First.bam.bai         17-0000-L,F-REPEAT.bam.bai

looks like centos has util-linux rename which doesn't support s/.../.../ but I am not sure how to adjust the rename in the script. Thank you Smilie.

rename -V
rename from util-linux 2.23.2

Last edited by cmccabe; 05-02-2019 at 10:34 AM.. Reason: added details
# 2  
First of all
rename s/"IonCode_[0-9][0-9][0-9][0-9]_"/""/g ...

works but looks misleading.
I would put the whole argument in quotes
rename "s/IonCode_[0-9][0-9][0-9][0-9]_//g" ...

Now to your question. The rename command is not portable. There are at least two different implementations in Linux distros.
Consult/compare the man pages!

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