Question

1

Rename multiple files with variable extensions to remove beginning and end of filename

rated 0 times [ 1] [ 0] / answers: 1 / hits: 1425 / 1 Year ago, sat, april 15, 2023, 10:41:09

I have multiple files I need to rename as below:

5891_1_0_AD3884_ACTCTCGA_S10.bam

5891_1_0_AD3884_ACTCTCGA_S10.bam.bai

5891_1_AD3875_GAGCTTGT_S1.bam

5891_1_AD3875_GAGCTTGT_S1.bam.bai

5891_2_AD3876_ACACGGTT_S2_R1.bam

5891_2_AD3876_ACACGGTT_S2_R2.bam.bai

I would like to remove everything except AD**** so that the resulting filenames would be:

AD3884.bam

AD3884.bam.bai

AD3875.bam

AD3875.bam.bai

AD3876.bam

AD3876.bam.bai

The number of underscores ("_") before and after the AD**** is not always consistent. Currently there are always 4 digits following the AD, but in the future it may increase to 5.

Ideally a bash solution from parameter expansion would be great (working in a Linux Ubuntu environment), though I have tried this without success. sed, awk, grep, or lastly rename solutions are also possible, though I have tried many versions of these without success. Any help would be much appreciated.

UPDATE

The rename solution from @steeldriver works perfectly.

I was able to make the solution from @Boba Fit work with the following modifications:

for file in *

do

 fn=AD"${file#*AD}"

 ext=${file#*.}

 mv $file rename/${fn%%_*}.${ext}

done

New edit

One additional issue is that the AD may also be lowercase (ad). For example:

5891_1_0_ad3884_ACTCTCGA_S10.bam

5891_1_0_ad3884_ACTCTCGA_S10.bam.bai

5891_1_AD3875_GAGCTTGT_S1.bam

5891_1_AD3875_GAGCTTGT_S1.bam.bai

5891_2_AD3876_ACACGGTT_S2_R1.bam

5891_2_AD3876_ACACGGTT_S2_R2.bam.bai

For the final result its ok if they are all capitalized (AD):

AD3884.bam

AD3884.bam.bai

AD3875.bam

AD3875.bam.bai

AD3876.bam

AD3876.bam.bai

But I need to be able to recognize upper and lowercase (case-insensitive) in the input.

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answered 1 Year ago lowovey · Accepted Answer

I've written a bash script for you

#!/bin/bash

for file in *

do

 name=$(echo "$file" | tr '[:lower:]' '[:upper:]')

 name=AD${name#*_AD}

 name=${name::6}

 extension=${file#*.}

 mv ${file} ${name}.${extension}

done

With # I remove all the (smallest possible) part in front of the string that matchs *_AD.
In the next line I cut the Sting in max length to 6.
I write the extension by remogin the smales part that matches *..

Then we move the file to ${name}.${extension}.

Hope it works well.