How to apply for loop in bash terminal

Question

I am new to bash and would like to get help how to run for loop.

Here is my question, I have 10 different sorted bam files(*.sorted.bam) and I would like to do indexing for each sorted bam files.

I know how to run it for single file using the command below

samtools index sample.sorted.bam

I would be happy if some one could show me how to run for multiple files

Best, Amare

DustInComp · Accepted Answer · 2021-11-16 11:14:49Z

2

you can use the for..in loop like this:

for file in *.sorted.bam
do
  samtools index "$file"
done

or in a single line:

for file in *.sorted.bam; do samtools index "$file"; done

answered Nov 16, 2021 at 11:06

DustInComp

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2 Comments

Iterating over the output of ls is not quite desirable: mywiki.wooledge.org/… In this particular case using the glob pattern directly is better.

@IonuțG.Stan Edited the answer.